Functional genomics using crispr-cas systems, compositions, methods, screens and applications thereof

ABSTRACT

The present invention generally relates to libraries, compositions, methods, applications, kits and screens used in functional genomics that focus on gene function in a cell and that may use vector systems and other aspects related to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas systems and components thereof. Provided are vectors and vector systems, some of which encode one or more components of a CRISPR complex, as well as methods for the design and use of such vectors. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system.

RELATED APPLICATIONS AND INCORPORATION BY REFERENCE

This application is a continuation of U.S. application Ser. No. 14/973,062, filed on Dec. 17, 2015, which is a continuation-in-part of International Application No. PCT/US14/041806, filed on Jun. 10, 2014, which claims priority to U.S. provisional patent applications 61/836,123, 61/960,777 and 61/995,636, filed on Jun. 17, 2013, Sep. 25, 2013 and Apr. 15, 2014 respectively, each incorporated herein by reference. This application is also a continuation of International Application No. PCT/US13/74800, filed Dec. 12, 2013. For purposes of the United States, this application also can be a continuation-in-part of PCT/US13/74800, filed Dec. 12, 2013; and Applicants reserve as permitted under US law to claim in the United States any right or benefit to U.S. provisional application 61/802,174, filed Mar. 15, 2013 and/or 61/736,527, filed Dec. 12, 2012, which are in the lineage of PCT/US13/74800, filed Dec. 12, 2013.

The foregoing applications, and all documents cited therein or during their prosecution (“appin cited documents”) and all documents cited or referenced in the appin cited documents, and all documents cited or referenced herein (“herein cited documents”), and all documents cited or referenced in herein cited documents, together with any manufacturer's instructions, descriptions, product specifications, and product sheets for any products mentioned herein or in any document incorporated by reference herein, are hereby incorporated herein by reference, and may be employed in the practice of the invention. More specifically, all referenced documents are incorporated by reference to the same extent as if each individual document was specifically and individually indicated to be incorporated by reference.

The foregoing patent applications, from which this application claims priority, expressly refers to a lengthy table section. Copies of the Tables have been submitted in triplicate in compact disc form (i.e., “Copy 1,” “Copy 2” and “Copy 3”) with the USPTO on Apr. 15, 2014 in connection with the filing of U.S. provisional application 61/995,636 and are hereby incorporated herein by reference in their entirety, and may be employed in the practice of the invention. Each compact disc (CD), created Apr. 11, 2014, contains the following files:

-   -   Table 1_hKO 65K sgRNAs with off-target scores.txt, 3,883,008         bytes     -   Table 2A_Human GeCKOv2 controls.txt, 53,248 bytes     -   Table 2B_Human GeCKOv2 controls.txt, 77,824 bytes     -   Table 3_Human GeCKOv2 exons A.txt, 8,069,120 bytes     -   Table 4_Human GeCKOv2 exons B.txt, 8,081,408 bytes     -   Table 5_Human GeCKOv2 miRNAs.txt, 331,776 bytes     -   Table 6_Mouse GeCKOv2 controls.txt, 610,304 bytes     -   Table 7_Mouse GeCKOv2 exons A.txt, 8,650,752 bytes     -   Table 8_Mouse GeCKOv2 exons B.txt, 8,671,232 bytes     -   Table 9_Mouse GeCKOv2 miRNAs.txt, 208,896 bytes

The disclosure in each of the foregoing US provisional patent applications is particularly incorporated herein by reference and particularly the disclosure of the CDs filed with 61/960,777 and 61/995,636 is particularly incorporated herein by reference in their entirety and is also included in this disclosure by way of the Biological Deposit(s) with the ATCC of plasmids/plasmid library(ies) containing nucleic acid molecules encoding selected guide sequences having the information set forth in U.S. provisional patent applications 61/960,777 and 61/995,636, namely, Deposit Nos: PTA-121339, PTA-121340, PTA-121341, PTA-121342, PTA-121343, deposited on Jun. 10, 2014, with the American Type Culture Collection on American Type Culture Collection (ATCC), 10801 University Boulevard, Manassas, Va. 20110 USA, under and pursuant to the terms of the Budapest Treaty. Upon issuance of a patent, all restrictions upon the Deposit(s) will be irrevocably removed, and the Deposit(s) is/are intended to meet the requirements of 37 CFR §§ 1.801-1.809. The Deposit(s) will be maintained in the depository for a period of 30 years, or 5 years after the last request, or for the effective, enforceable life of the patent, whichever is longer, and will be replaced if necessary during that period; and the requirements of 37 CFR §§ 1.801-1.809 are are met.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

This invention was made with government support under Grant No. MH100706 awarded by the National Institutes of Health. The government has certain rights in the invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on May 29, 2018, is named 114203-5001 SL.txt and is 162,193 bytes in size.

FIELD OF THE INVENTION

The present invention generally relates to libraries, compositions, methods, applications, kits and screens used in functional genomics that focus on gene function in a cell and that may use vector systems and other aspects related to Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas systems and components thereof.

BACKGROUND OF THE INVENTION

Recent advances in genome sequencing techniques and analysis methods have significantly accelerated the ability to catalog and map genetic factors associated with a diverse range of biological functions and diseases. Functional genomics is a field of molecular biology that may be considered to utilize the vast wealth of data produced by genomic projects (such as genome sequencing projects) to describe gene (and protein) functions and interactions. Contrary to classical genomics, functional genomics focuses on the dynamic aspects such as gene transcription, translation, and protein-protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures, though these static aspects are very important and supplement one's understanding of cellular and molecular mechanisms. Functional genomics attempts to answer questions about the function of DNA at the levels of genes, RNA transcripts, and protein products. A key characteristic of functional genomics studies is a genome-wide approach to these questions, generally involving high-throughput methods rather than a more traditional “gene-by-gene” approach. Given the vast inventory of genes and genetic information it is advantageous to use genetic screens to provide information of what these genes do, what cellular pathways they are involved in and how any alteration in gene expression can result in particular biological process. Functional genomic screens attempt to characterize gene function in the context of living cells and hence are likely to generate biologically significant data. There are three key elements for a functional genomics screen: a good reagent to perturb the gene, a good tissue culture model and a good readout of cell state.

A reagent that has been used for perturbing genes in a number of functional genomics screens is RNA interference (RNAi). One can perform loss-of-function genetic screens and facilitate the identification of components of cellular signaling pathways utilizing RNAi. Gene silencing by RNAi in mammalian cells using small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) has become a valuable genetic tool. Development of efficient and robust approaches to perform genome scale shRNA screens have been described in Luo B et al., “Highly parallel identification of essential genes in cancer cells” Proc Natl Acad Sci USA. 2008 Dec. 23; 105(51):20380-5; Paddison P J et al., “A resource for large-scale RNA-interference-based screens in mammals” Nature. 2004 Mar. 25; 428(6981):427-31; Berns K et al., “A large-scale RNAi screen in human cells identifies new components of the p53 pathway” Nature. 2004 Mar. 25; 428(6981):431-7, the contents of all of which are incorporated by reference herein in their entirety.

However there are aspects of using shRNAs for functional genomic screens that are not advantageous. For example, there may be off-target effects for the shRNAs that limit spatial control. It is also important to note that using RNAi or other current technologies in functional genomics screens as mentioned herein results in a gene knockdown and not a gene knockout. Another minor factor that may be considered is the need for the continued expression of shRNA. Hence, there remains a need for new genome engineering technologies that are affordable, easy to set up, scalable, and amenable to knockout genes for de novo loss of function and afford spatial and temporal control with minimal off-target activity in a eukaryotic genome.

SUMMARY OF THE INVENTION

There exists a pressing need for alternative and robust systems and techniques for sequence targeting in functional genomic screens and other applications thereof. This invention addresses this need and provides related advantages. The CRISPR/Cas or the CRISPR-Cas system (both terms are used interchangeably throughout this application) does not require the generation of customized proteins (as in the case of technologies involving zinc finger proteins, meganucleases or transcription activator like effectors (TALEs)) to target specific sequences but rather a single Cas enzyme can be programmed by a short RNA molecule to recognize a specific DNA target, in other words the Cas enzyme can be recruited to a specific DNA target using said short RNA molecule. This enables parallel targeting of thousands of genomic loci using oligo library synthesis. Adding the CRISPR-Cas system to the repertoire of functional genomics tools and analysis methods may significantly simplify the methodology and accelerate the ability to catalog and map genetic factors associated with a diverse range of biological functions and diseases. The CRISPR-Cas system can be used effectively for gene targeting and knockout without deleterious effects in functional genomic screens and other applications thereof.

Aspects of the invention relate to synthesizing different unique 20 bp spacer or guide RNA sequences with which different genomic locations can be targeted with double strand breaks (DSBs) and indel mutations. It is this easy programmability that makes CRISPR an attractive targeted screening system. As with pooled shRNA libraries, array oligonucleotide synthesis technologies allow for parallel synthesis of thousands of targeting sequences that can be cloned en masse into a vector, e.g. a viral vector such as an AAV vector or a lentiviral vector, and produced as virus in a pool. This allows for targeting of the Cas9 nuclease by modification of a 20 nt RNA guide sequence and genetic perturbation on the level of the genome itself.

In one aspect, the invention provides a genome wide library comprising a plurality of unique CRISPR-Cas system guide sequences that are capable of targeting a plurality of target sequences in genomic loci, wherein said targeting results in a knockout of gene function. Aspects of the invention include the guide sequences listed in Tables 1, 3, 4, 5, 7, 8 or 9.

Aspects of the invention, including libraries, methods and kits also expressly include the library and guide sequences as described in “Genome-scale CRISPR-Cas9 knockout screening in human cells”, Shalem O, Sanjana N E, Hartenian E, Shi X, Scott D A, Mikkelsen T S, Heckl D, Ebert B L, Root D E, Doench J G, Zhang F., Science. 2014 Jan. 3; 343(6166):84-7, including all and any disclosure therof and all and any disclosure from the corresponding Supplementary materials available from the publisher, including Supplementary materials made available online.

Aspects of the invention, including libraries, methods and kits also expressly include the libraries and guide sequences as described on the addgene website, accessible at http://www.addgene.org/CRISPR/libraries/, under “Feng Zhang Lab (targets human genes)”, including the GeCKO v1 and GeCKO v2 libraries. These libraries are alternatively referred to herein as GeCKO1 and GeCKO2. Those libraries are also disclosure in each of the priority U.S. provisional patent applications 61/960,777, 61/961,980, 61/963,643 and 61/995,636, and especially the CDs filed therewith, and the Budapest Treaty Biological Deposit(s) with the ATCC in connection with this application; namely, ATCC Deposit Nos: PTA-121339, PTA-121340, PTA-121341, PTA-121342, PTA-121343.

In one aspect, the invention provides a CRISPR library for use in a method of knocking out in parallel every gene in the genome. In one aspect, the library or libraries consist of specific sgRNA sequences for gene knock-out in either the human or mouse genome. In one aspect, each species-specific library is delivered as two half-libraries (e.g., A and B). In one aspect, when used together, the A and B libraries contain 6 sgRNAs per gene (3 sgRNAs in each half library). In one aspect, each library or half library may comprise up to 4 sgRNAs per microRNA (“miRNA”). In one aspect, each species-specific library comprises sgRNA specific for each of over 1000 miRNA per genome (e.g., 1864 in human, 1175 in mouse). In one aspect, each species-specific library comprises at least one, preferably at least 3, and most preferably at least 6 sgRNA specific to each gene in the targeted genome (e.g., 19,052 in human, 20,661 in mouse).

In one aspect, the GeCKO library is packaged in a viral vector. In one aspect, the GeCKO library is packaged in a lentivirus vector. In one aspect, the packaged GeCKO library is transduced at an MOI (multiplicity of infection) of about 10, of about 5, of about 3, of about 1 or of about less than 1, about less than 0.75, about less than 0.5, about less than 0.4, about less than 0.3, about less than 0.2 or about less than 0.1. In a further embodiment the cell is transduced with a multiplicity of infection (MOI) of 0.3-0.75, preferably, the MOI has a value close to 0.4, more preferably the MOI is 0.3 or 0.4. In one aspect, the MOI is about 0.3 or 0.4, thereby creating a panel of cells comprising about 1 CRISPR-Cas system chimeric RNA (chiRNA) per cell, after appropriate selection for successfully transfected/transduced cells, thereby providing a panel of cells comprising a cellular library with parallel knock outs of every gene in the genome.

In another aspect, the invention provides for a method of knocking out in parallel every gene in the genome, the method comprising contacting a population of cells with a composition comprising a vector system comprising one or more packaged vectors comprising

a) a first regulatory element operably linked to a CRISPR-Cas system chimeric RNA (chiRNA) polynucleotide sequence that targets a DNA molecule encoding a gene product,

wherein the polynucleotide sequence comprises

(a) a guide sequence capable of hybridizing to a target sequence,

(b) a tracr mate sequence, and

(c) a tracr sequence, and

b) a second regulatory element operably linked to a sequence encoding a Cas protein and a selection marker, wherein components (a) and (b) are located on same or different vectors of the system, wherein each cell is transfected with a single packaged vector, selecting for successfully transfected cells, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to a target sequence in the genomic loci of the DNA molecule encoding the gene product, wherein the CRISPR complex comprises a CRISPR enzyme complexed with (1) the guide sequence that is hybridizable to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence, wherein the guide sequence is selected from the library of the invention, wherein the guide RNAs target the genomic loci of the DNA molecule encoding the gene product and the CRISPR enzyme cleaves the genomic loci of the DNA molecule encoding the gene product and whereby each cell in the population of cells has a unique gene knocked out in parallel. In preferred embodiments, the cell is a eukaryotic cell. In further embodiments the vector is a lentivirus, a adenovirus or a AAV and/or the first regulatory element is a Pol III promoter such as a H1 promoter and a U6 promoter and/or the second regulatory element is a Pol II promoter selected from a doxycycline inducible promoter, a cell-type specific promoter and an EFS promoter, and/or the vector system comprises one vector and/or the CRISPR enzyme is Cas9.

The invention also encompasses methods of selecting individual cell knock outs that survive under a selective pressure, the method comprising

contacting a population of cells with a composition comprising a vector system comprising one or more packaged vectors comprising a) a first regulatory element operably linked to a CRISPR-Cas system chimeric RNA (chiRNA) polynucleotide sequence that targets a DNA molecule encoding a gene product,

wherein the polynucleotide sequence comprises

(a) a guide sequence capable of hybridizing to a target sequence,

(b) a tracr mate sequence, and

(c) a tracr sequence, and

b) a second regulatory element operably linked to a Cas protein and a selection marker, wherein components (a) and (b) are located on same or different vectors of the system, wherein each cell is transfected with a single packaged vector, selecting for successfully transfected cells, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to a target sequence in the genomic loci of the DNA molecule encoding the gene product, wherein the CRISPR complex comprises a CRISPR enzyme complexed with (1) the guide sequence that is hybridizable to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence, wherein the guide sequence is selected from the library of the invention, wherein the guide RNAs target the genomic loci of the DNA molecule encoding the gene product and the CRISPR enzyme cleaves the genomic loci of the DNA molecule encoding the gene product, whereby each cell in the population of cells has a unique gene knocked out in parallel, applying the selective pressure, and selecting the cells that survive under the selective pressure.

In preferred embodiments, the selective pressure is application of a drug, FACS sorting of cell markers or aging and/or the vector is a lentivirus, a adenovirus or a AAV and/or the first regulatory element is a Pol III promoter such as a H1 promoter and a U6 promoter and/or the second regulatory element is a Pol II promoter selected from a doxycycline inducible promoter, a cell-type specific promoter and an EFS promoter, and/or the vector system comprises one vector and/or the CRISPR enzyme is Cas9.

In other aspects, the invention encompasses methods of identifying the genetic basis of one or more medical symptoms exhibited by a subject, the method comprising

obtaining a biological sample from the subject and isolating a population of cells having a first phenotype from the biological sample; contacting the cells having the first phenotype with a composition comprising a vector system comprising one or more packaged vectors comprising a) a first regulatory element operably linked to a CRISPR-Cas system chimeric RNA (chiRNA) polynucleotide sequence that targets a DNA molecule encoding a gene product,

wherein the polynucleotide sequence comprises

(a) a guide sequence capable of hybridizing to a target sequence,

(b) a tracr mate sequence, and

(c) a tracr sequence, and

b) a second regulatory element operably linked to a Cas protein and a selection marker, wherein components (a) and (b) are located on same or different vectors of the system, wherein each cell is transfected with a single packaged vector, selecting for successfully transfected cells, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to a target sequence in the genomic loci of the DNA molecule encoding the gene product, wherein the CRISPR complex comprises a CRISPR enzyme complexed with (1) the guide sequence that is hybridizable to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence, wherein the guide sequence is selected from the library of the invention, wherein the guide RNAs target the genomic loci of the DNA molecule encoding the gene product and the CRISPR enzyme cleaves the genomic loci of the DNA molecule encoding the gene product, whereby each cell in the population of cells has a unique gene knocked out in parallel, applying the selective pressure, selecting the cells that survive under the selective pressure, determining the genomic loci of the DNA molecule that interacts with the first phenotype and identifying the genetic basis of the one or more medical symptoms exhibited by the subject.

In preferred embodiments, the selective pressure is application of a drug, FACS sorting of cell markers or aging and/or the vector is a lentivirus, a adenovirus or a AAV and/or the first regulatory element is a Pol III promoter such as a H1 promoter and a U6 promoter and/or the second regulatory element is a Pol II promoter selected from a doxycycline inducible promoter, a cell-type specific promoter and an EFS promoter, and/or the vector system comprises one vector and/or the CRISPR enzyme is Cas9.

The invention also comprehends kit comprising the library of the invention. In certain aspects, the kit comprises a single container comprising one or more vectors comprising the library of the invention. In other aspects, the kit comprises a single container comprising one or more plasmids comprising the library of the invention. The invention also comprehends kits comprising a panel comprising a selection of unique CRISPR-Cas system guide sequences from the library of the invention, wherein the selection is indicative of a particular physiological condition. In preferred embodiments, the targeting is of about 100 or more sequences, about 1000 or more sequences or about 20,000 or more sequences or the entire genome. In other embodiments a panel of target sequences is focused on a relevant or desirable pathway, such as an immune pathway or cell division.

In one aspect, the invention provides a genome wide library comprising a plurality of unique CRISPR-Cas system guide sequences that are capable of targeting a plurality of target sequences in genomic loci of a plurality of genes, wherein said targeting results in a knockout of gene function. In preferred embodiments of the invention the unique CRISPR-Cas system guide sequences are selected by an algorithm that predicts the efficacy of the guide sequences based on the primary nucleotide sequence of the guide sequence and/or by a heuristic that ranks the guide sequences based on off target scores. In certain embodiments of the invention, the guide sequences are capable of targeting a plurality of target sequences in genomic loci of a plurality of genes selected from the entire genome. In embodiments, the genes may represent a subset of the entire genome; for example, genes relating to a particular pathway (for example, an enzymatic pathway) or a particular disease or group of diseases or disorders may be selected. One or more of the genes may include a plurality of target sequences; that is, one gene may be targeted by a plurality of guide sequences. In certain embodiments, a knockout of gene function is not essential, and for certain applications, the invention may be practiced where said targeting results only in a knockdown of gene function. However, this is not preferred.

Aspects of the invention may include the guide sequences listed in Tables 1, 3, 4, 5, 7, 8 or 9 as provided in the compact discs created Apr. 11, 2014, as filed in connection with U.S. applications 61/960,777 and 61/995,636. In a further embodiment, the guide sequences target constitutive exons downstream of a start codon of the gene. In an advantageous embodiment, the guide sequences target either a first or a second exon of the gene. In yet another embodiment, the guide sequences target a non-transcribed strand of the genomic loci of the gene.

In another aspect, the invention provides for a method of knocking out in parallel every gene in the genome, the method comprising contacting a population of cells with a composition comprising a vector system comprising one or more packaged vectors comprising a) a first regulatory element operably linked to a CRISPR-Cas system chimeric RNA (chiRNA) polynucleotide sequence that targets a DNA molecule encoding a gene product,

wherein the polynucleotide sequence comprises

(a) a guide sequence capable of hybridizing to a target sequence,

(b) a tracr mate sequence, and

(c) a tracr sequence, and

b) a second regulatory element operably linked to a Cas protein and a selection marker, wherein components (a) and (b) are located on same or different vectors of the system, wherein each cell is transduced with a single packaged vector, selecting for successfully transduced cells, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to a target sequence in the genomic loci of the DNA molecule encoding the gene product, wherein the CRISPR complex comprises a CRISPR enzyme complexed with (1) the guide sequence that is hybridizable to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence, wherein the guide sequence is selected from the library of the invention, wherein the guide sequence targets the genomic loci of the DNA molecule encoding the gene product and the CRISPR enzyme cleaves the genomic loci of the DNA molecule encoding the gene product and whereby each cell in the population of cells has a unique gene knocked out in parallel. In preferred embodiments, the cell is a eukaryotic cell. The eukaryotic cell may be a plant or animal cell; for example, algae or microalgae; vertebrate, preferably mammalian, including murine, ungulate, primate, human; insect. In further embodiments the vector is a lentivirus, an adenovirus or an AAV and/or the first regulatory element is a Pol III promoter such as a H1 promoter and a U6 promoter and/or the second regulatory element is a Pol II promoter such as an EFS promoter or a doxycycline inducible promoter or a cell-type specific promoter as further described herein, and/or the vector system comprises one vector and/or the CRISPR enzyme is Cas9. In aspects of the invention the cell is a eukaryotic cell, preferably a human cell. In a further embodiment the cell is transduced with a multiplicity of infection (MOI) of 0.3-0.75, preferably, the MOI has a value close to 0.4, more preferably the MOI is 0.3 or 0.4.

The invention also encompasses methods of selecting individual cell knock outs that survive under a selective pressure, the method comprising contacting a population of cells with a composition comprising a vector system comprising one or more packaged vectors comprising

a) a first regulatory element operably linked to a CRISPR-Cas system chimeric RNA (chiRNA) polynucleotide sequence that targets a DNA molecule encoding a gene product, wherein the polynucleotide sequence comprises

(a) a guide sequence capable of hybridizing to a target sequence,

(b) a tracr mate sequence, and

(c) a tracr sequence, and

b) a second regulatory element operably linked to a Cas protein and a selection marker, wherein components (a) and (b) are located on same or different vectors of the system, wherein each cell is transduced with a single packaged vector, selecting for successfully transduced cells, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to a target sequence in the genomic loci of the DNA molecule encoding the gene product, wherein the CRISPR complex comprises a CRISPR enzyme complexed with (1) the guide sequence that is hybridizable to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence, wherein the guide sequence is selected from the library of the invention, wherein the guide sequence targets the genomic loci of the DNA molecule encoding the gene product and the CRISPR enzyme cleaves the genomic loci of the DNA molecule encoding the gene product, whereby each cell in the population of cells has a unique gene knocked out in parallel, applying the selective pressure, and selecting the cells that survive under the selective pressure. In preferred embodiments, the selective pressure is application of a drug, FACS sorting of cell markers or aging and/or the vector is a lentivirus, a adenovirus or a AAV and/or the first regulatory element is a Pol III promoter such as a H1 promoter and a U6 promoter and/or the second regulatory element is a Pol II promoter such as an EFS promoter or a doxycycline inducible promoter or a cell-type specific promoter, and/or the vector system comprises one vector and/or the CRISPR enzyme is Cas9. In a further embodiment the cell is transduced with a multiplicity of infection (MOI) of 0.3-0.75, preferably, the MOI has a value close to 0.4, more preferably the MOI is 0.3 or 0.4. In aspects of the invention the cell is a eukaryotic cell. The eukaryotic cell may be a plant or animal cell; for example, algae or microalgae; vertebrate, preferably mammalian, including murine, ungulate, primate, human; insect. Preferably the cell is a human cell. In preferred embodiments of the invention, the method further comprises extracting DNA and determining the depletion or enrichment of the guide sequences by deep sequencing.

In other aspects, the invention encompasses methods of identifying the genetic basis of one or more medical symptoms exhibited by a subject, the method comprising obtaining a biological sample from the subject and isolating a population of cells having a first phenotype from the biological sample;

contacting the cells having the first phenotype with a composition comprising a vector system comprising one or more packaged vectors comprising a) a first regulatory element operably linked to a CRISPR-Cas system chimeric RNA (chiRNA) polynucleotide sequence that targets a DNA molecule encoding a gene product,

wherein the polynucleotide sequence comprises

(a) a guide sequence capable of hybridizing to a target sequence,

(b) a tracr mate sequence, and

(c) a tracr sequence, and

b) a second regulatory element operably linked to a Cas protein and a selection marker, wherein components (a) and (b) are located on same or different vectors of the system, wherein each cell is transduced with a single packaged vector, selecting for successfully transduced cells, wherein when transcribed, the tracr mate sequence hybridizes to the tracr sequence and the guide sequence directs sequence-specific binding of a CRISPR complex to a target sequence in the genomic loci of the DNA molecule encoding the gene product, wherein the CRISPR complex comprises a CRISPR enzyme complexed with (1) the guide sequence that is hybridizable to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence, wherein the guide sequence is selected from the library of the invention, wherein the guide sequence targets the genomic loci of the DNA molecule encoding the gene product and the CRISPR enzyme cleaves the genomic loci of the DNA molecule encoding the gene product, whereby each cell in the population of cells has a unique gene knocked out in parallel, applying a selective pressure, selecting the cells that survive under the selective pressure, determining the genomic loci of the DNA molecule that interacts with the first phenotype and identifying the genetic basis of the one or more medical symptoms exhibited by the subject. In preferred embodiments, the selective pressure is application of a drug, FACS sorting of cell markers or aging and/or the vector is a lentivirus, an adenovirus or an AAV and/or the first regulatory element is a Pol III promoter such as a H1 promoter and a U6 promoter and/or the second regulatory element is a Pol II promoter such as an EFS promoter or a doxycycline inducible promoter or a cell-type specific promoter, and/or the vector system comprises one vector and/or the CRISPR enzyme is Cas9. In a further embodiment the cell is transduced with a multiplicity of infection (MOI) of 0.3-0.75, preferably, the MOI has a value close to 0.4, more preferably the MOI is 0.3 or 0.4. In aspects of the invention the cell is a eukaryotic cell, preferably a human cell.

In an aspect, the library of the invention is a plasmid library. The plasmid library (preferably as further cloned into a delivery vector, such as lentivector) may be selected from the group consisting of:

-   -   (A) GeCKO1—library of sgRNA plasmids each encoding selected         guide sequences and cloned into vector (lentiCRISPRv2)—ATCC         Deposit No. PTA-121339;     -   (B) GeCKO2—half library A (human) sgRNA plasmids each encoding         selected guide sequences and cloned into vector—ATCC Deposit No.         PTA-121340;     -   (C) GeCKO2—half library B (human) of sgRNA plasmids each         encoding selected guide sequences and cloned into vector—ATCC         Deposit No. PTA-121341;     -   (D) GeCKO2—half library A (mouse) sgRNA plasmids each encoding         selected guide sequences and cloned into vector—ATCC Deposit No.         PTA-121342; and     -   (E) GeCKO2—half library A (mouse) sgRNA plasmids each encoding         selected guide sequences and cloned into vector—ATCC Deposit No.         PTA-121343;         wherein “GeCKO” stands for Genome-scale CRISPR-Cas9 Knock Out”.         The various GeCKO libraries have been generated for targeting         either human or mouse genomes and consist of a one vector system         or a two vector system for delivery of short 20 bp sequences of         the sgRNA with or without Cas9. The GeCKO1 library consists of         specific sgRNA sequences for gene knock-out in either the human         or mouse genome. The GeCKO2 libraries consist of specific sgRNA         sequences for gene knock-out in either the human or mouse         genome, wherein each species-specific library is delivered as         two half-libraries (A and B). When used together, the A and B         libraries contain 6 sgRNAs per gene (3 sgRNAs in each library)         and may contain 4 sgRNAs per microRNA (“miRNA”) for over 1000         miRNA per genome (1864 in human, 1175 in mouse). Any one or more         GeCKO library may be used in any one of the methods or in any         one of the kits of the present invention. The GeCKO libraries,         and specifically each of (A) to (E), above, were deposited with         the American Type Culture Collection (ATCC) on Jun. 10, 2014,         and are further exemplified in ATCC Deposit Nos: PTA-121339,         PTA-121340, PTA-121341, PTA-121342, PTA-121343, deposited on         Jun. 10, 2014, as provided herein and in the compact discs         created Apr. 11, 2014, as filed in connection with U.S.         applications 61/960,777 and 61/995,636, including as the         information set forth in those US applications and the compact         discs filed therewith is presented herein via the ATCC Deposits.

In an aspect, the vector systems in the methods of the invention comprise one or more lentiviral vector(s). In a preferred embodiment, the one or more lentiviral vectors may comprise a codon optimized nuclear localization signal (NLS), a codon optimized P2A bicistronic linker sequence and an optimally placed U6 driven guide RNA cassette. In another aspect the vector system comprises two lentiviral vectors, wherein one lentiviral vector comprises the Cas9 enzyme and the other lentiviral vector comprises the guide RNA selected from the libraries of the invention. In an embodiment of the invention, each vector has a different selection marker, e.g. a different antibiotic resistance marker. The invention also comprehends kits comprising the libraries of the invention. In certain aspects, the kit comprises a single container comprising vectors comprising the library of the invention. In other aspects, the kit comprises a single container comprising plasmids comprising the library of the invention. The invention also comprehends kits comprising a panel comprising a selection of unique CRISPR-Cas system guide sequences from the library of the invention, wherein the selection is indicative of a particular physiological condition. In preferred embodiments, the targeting is of about 100 or more sequences, about 1000 or more sequences or about 20,000 or more sequences or the entire genome. In other embodiments a panel of target sequences is focused on a relevant or desirable pathway, such as an immune pathway or cell division.

In an aspect, the invention provides a non-human eukaryotic organism; preferably a multicellular eukaryotic organism, comprising a eukaryotic host cell according to any of the described embodiments in which a candidate gene is knocked down or knocked out. Preferably the gene is knocked out. In other aspects, the invention provides a eukaryotic organism; preferably a multicellular eukaryotic organism, comprising a eukaryotic host cell which has been altered according to any of the described embodiments. The organism in some embodiments of these aspects may be an animal; for example a mammal. Also, the organism may be an arthropod such as an insect. The organism also may be a plant. Further, the organism may be a fungus. In some embodiments, the invention provides a set of non-human eukaryotic organisms, each of which comprises a eukaryotic host cell according to any of the described embodiments in which a candidate gene is knocked down or knocked out. In preferred embodiments, the set comprises a plurality of organisms, in each of which a different gene is knocked down or knocked out.

In some embodiments, the CRISPR enzyme comprises one or more nuclear localization sequences of sufficient strength to drive accumulation of said CRISPR enzyme in a detectable amount in the nucleus of a eukaryotic cell. In some embodiments, the CRISPR enzyme is a type II CRISPR system enzyme. In some embodiments, the CRISPR enzyme is a Cas9 enzyme. In some embodiments, the Cas9 enzyme is S. pneumoniae, S. pyogenes or S. thermophilus Cas9, and may include mutated Cas9 derived from these organisms. The enzyme may be a Cas9 homolog or ortholog. In some embodiments, the CRISPR enzyme is codon-optimized for expression in a eukaryotic cell. In some embodiments, the CRISPR enzyme directs cleavage of one or two strands at the location of the target sequence. In one aspect, the CRISPR enzyme comprises at least one mutation in a catalytic domain. In one aspect, the CRISPR enzyme is a nickase. In some embodiments, the CRISPR enzyme lacks DNA strand cleavage activity. In some embodiments, the first regulatory element is a polymerase III promoter. In some embodiments, the second regulatory element is a polymerase II promoter. In some embodiments, the guide sequence is at least 15, 16, 17, 18, 19, 20, 25 nucleotides, or between 10-30, or between 15-25, or between 15-20 nucleotides in length. In an advantageous embodiment the guide sequence is 20 nucleotides in length.

As mentioned previously, a critical aspect of the invention is gene knock-out and not knock-down (which can be done with genome-wide siRNA or shRNA libraries). Applicants have provided the first demonstration of genome-wide knockouts that are barcoded and can be easily readout with next generation sequencing. Every single gene (or a subset of desired genes, for example, those relating to a particular enzymatic pathway or the like (e.g., including but not limited to pathways involved in signaling, metabolism, gene regulation, immune response, disease resistance, drug response and/or resistance, etc.) may be knocked OUT in parallel. This allows quantification of how well each gene KO confers a survival advantage with the selective pressure of the screen. In a preferred embodiment, the invention has advantageous pharmaceutical application, e.g., the invention may be harnessed to test how robust any new drug designed to kill cells (e.g. chemotherapeutic) is to mutations that KO genes. Cancers mutate at an exceedingly fast pace and the libraries and methods of the invention may be used in functional genomic screens to predict the ability of a chemotherapy to be robust to “escape mutations”. (Refer to PLX data in BRAF V600E mutant A375 cells in Example 9. Other mutations (e.g. NF1, NF2, and MED12) allow escape from the killing action of PLX.)

Aspects of the invention comprehend many types of screens and selection mechanisms can also be used with CRISPR screening. Screens for resistance to viral or bacterial pathogens may be used to identify genes that prevent infection or pathogen replication. As in drug resistance screens, survival after pathogen exposure provides strong selection. In cancer, negative selection CRISPR screens may identify “oncogene addictions” in specific cancer subtypes that can provide the foundation for molecular targeted therapies. For developmental studies, screening in human and mouse pluripotent cells may pinpoint genes required for pluripotency or for differentiation into distinct cell types. To distinguish cell types, fluorescent or cell surface marker reporters of gene expression may be used and cells may be sorted into groups based on expression level. Gene-based reporters of physiological states, such as activity-dependent transcription during repetitive neural firing or from antigen-based immune cell activation, may also be used. Any phenotype that is compatible with rapid sorting or separation may be harnessed for pooled screening. CRISPR screening may also be used as a diagnostic tool: With patient-derived iPS cells, genome-wide libraries may be used to examine multi-gene interactions (similar to synthetic lethal screens) or how different loss-of-functions mutations accumulated through aging or disease can interact with particular drug treatments.

Accordingly, it is an object of the invention not to encompass within the invention any previously known product, process of making the product, or method of using the product such that Applicants reserve the right and hereby disclose a disclaimer of any previously known product, process, or method. It is further noted that the invention does not intend to encompass within the scope of the invention any product, process, or making of the product or method of using the product, which does not meet the written description and enablement requirements of the USPTO (35 U.S.C. § 112, first paragraph) or the EPO (Article 83 of the EPC), such that Applicants reserve the right and hereby disclose a disclaimer of any previously described product, process of making the product, or method of using the product.

It is noted that in this disclosure and particularly in the claims and/or paragraphs, terms such as “comprises”, “comprised”, “comprising” and the like can have the meaning attributed to it in U.S. patent law; e.g., they can mean “includes”, “included”, “including”, and the like; and that terms such as “consisting essentially of” and “consists essentially of” have the meaning ascribed to them in U.S. patent law, e.g., they allow for elements not explicitly recited, but exclude elements that are found in the prior art or that affect a basic or novel characteristic of the invention. These and other embodiments are disclosed or are obvious from and encompassed by, the following Detailed Description.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:

FIG. 1 shows a schematic model of the CRISPR system. The Cas9 nuclease from Streptococcus pyogenes (yellow) is targeted to genomic DNA by a synthetic guide RNA (sgRNA) consisting of a 20-nt guide sequence (blue) and a scaffold (red). The guide sequence base-pairs with the DNA target (blue), directly upstream of a requisite 5′-NGG protospacer adjacent motif (PAM; magenta), and Cas9 mediates a double-stranded break (DSB) ˜3 bp upstream of the PAM (red triangle).

FIG. 2A-2F shows an exemplary CRISPR system, a possible mechanism of action, an example adaptation for expression in eukaryotic cells, and results of tests assessing nuclear localization and CRISPR activity. FIG. 2C discloses SEQ ID NOS 79-80, respectively, in order of appearance. FIG. 2E discloses SEQ ID NOS 81-83, respectively, in order of appearance. FIG. 2F discloses SEQ ID NOS 84-88, respectively, in order of appearance.

FIG. 3A-3D shows results of an evaluation of SpCas9 specificity for an example target. FIG. 3A discloses SEQ ID NOS 89, 82 and 90-100, respectively, in order of appearance. FIG. 3C discloses SEQ ID NO: 89.

FIG. 4A-4G show an exemplary vector system and results for its use in directing homologous recombination in eukaryotic cells. FIG. 4E discloses SEQ ID NO: 101. FIG. 4F discloses SEQ ID NOS 102-103, respectively, in order of appearance. FIG. 4G discloses SEQ ID NOS 104-108, respectively, in order of appearance.

FIG. 5 provides a table of protospacer sequences and summarizes modification efficiency results for protospacer targets designed based on exemplary S. pyogenes and S. thermophilus CRISPR systems with corresponding PAMs against loci in human and mouse genomes. Cells were transfected with Cas9 and either pre-crRNA/tracrRNA or chimeric RNA, and analyzed 72 hours after transfection. Percent indels are calculated based on Surveyor assay results from indicated cell lines (N=3 for all protospacer targets, errors are S.E.M., N.D. indicates not detectable using the Surveyor assay, and N.T. indicates not tested in this study). FIG. 5 discloses SEQ ID NOS 17, 16, 15, 109-114, 19, 18 and 115-119, respectively, in order of appearance.

FIG. 6A-6C shows a comparison of different tracrRNA transcripts for Cas9-mediated gene targeting. FIG. 6A discloses SEQ ID NOS 120 and 121, respectively, in order of appearance.

FIG. 7 shows a schematic of a surveyor nuclease assay for detection of double strand break-induced micro-insertions and micro-deletions.

FIG. 8A-8B shows exemplary bicistronic expression vectors for expression of CRISPR system elements in eukaryotic cells. FIG. 8A discloses SEQ ID NOS 122-124, respectively, in order of appearance. FIG. 8B discloses SEQ ID NOS 125-127, respectively, in order of appearance.

FIG. 9A-9C shows histograms of distances between adjacent S. pyogenes SF370 locus 1 PAM (NGG) (FIG. 9A) and S. thermophilus LMD9 locus 2 PAM (NNAGAAW) (FIG. 9B) in the human genome; and distances for each PAM by chromosome (Chr) (FIG. 9C).

FIG. 10A-10D shows an exemplary CRISPR system, an example adaptation for expression in eukaryotic cells, and results of tests assessing CRISPR activity. FIG. 10B discloses SEQ ID NOS 128-129, respectively, in order of appearance. FIG. 10C discloses SEQ ID NO: 130.

FIG. 11A-11C shows exemplary manipulations of a CRISPR system for targeting of genomic loci in mammalian cells. FIG. 11A discloses SEQ ID NO: 131. FIG. 11B discloses SEQ ID NO: 132-134, respectively, in order of appearance.

FIG. 12A-12B shows the results of a Northern blot analysis of crRNA processing in mammalian cells. FIG. 12A discloses SEQ ID NO: 135.

FIG. 13A-13B shows an exemplary selection of protospacers in the human PVALB (SEQ ID NO: 136) and mouse Th loci (SEQ ID NO: 137).

FIG. 14 shows example protospacer and corresponding PAM sequence targets of the S. thermophilus CRISPR system in the human EMX1 locus (SEQ ID NO: 130).

FIG. 15 provides a table of sequences for primers (SEQ ID NOS 138-147, respectively, in order of appearance) and probes (SEQ ID NOS 148-149, respectively, in order of appearance) used for Surveyor, RFLP, genomic sequencing, and Northern blot assays.

FIG. 16A-16C shows exemplary manipulation of a CRISPR system with chimeric RNAs and results of SURVEYOR assays for system activity in eukaryotic cells. FIG. 16A discloses SEQ ID NO: 150)

FIG. 17A-17B shows a graphical representation of the results of SURVEYOR assays for CRISPR system activity in eukaryotic cells.

FIG. 18 shows an exemplary visualization of some S. pyogenes Cas9 target sites in the human genome using the UCSC genome browser. FIG. 18 discloses SEQ ID NOS 151-229, respectively, in order of appearance.

FIG. 19A-19D shows a circular depiction of the phylogenetic analysis revealing five families of Cas9s, including three groups of large Cas9s (˜1400 amino acids) and two of small Cas9s (˜1100 amino acids).

FIG. 20A-20F shows the linear depiction of the phylogenetic analysis revealing five families of Cas9s, including three groups of large Cas9s (˜1400 amino acids) and two of small Cas9s (˜1100 amino acids).

FIG. 21A-21D (a-d) shows genome editing via homologous recombination. (a) Schematic of SpCas9 nickase, with D10A mutation in the RuvC I catalytic domain. (b) Schematic representing homologous recombination (HR) at the human EMXJ locus using either sense or antisense single stranded oligonucleotides as repair templates. Red arrow above indicates sgRNA cleavage site; PCR primers for genotyping (Tables J and K) are indicated as arrows in right panel. (c) Sequence of region modified by HR. FIG. 21C discloses SEQ ID NOS 230-232, 230, 233 and 232, respectively, in order of appearance. d, SURVEYOR assay for wildtype (wt) and nickase (D10A) SpCas9-mediated indels at the EMX1 target 1 locus (n=3). Arrows indicate positions of expected fragment sizes.

FIG. 22A-22B shows single vector designs for SpCas9. FIG. 22A discloses SEQ ID NOS 234-236, respectively, in order of appearance. FIG. 22B discloses SEQ ID NO: 237.

FIG. 23A-23D shows A) Design of sgRNAs for functional knock-out of all coding genes in the human genome. Early constitutive exons for genes are identified using Illumina Human BodyMap 2.0 and NCBI CCDS datasets. sgRNAs are ranked by an off-target score using a metric that includes the number of off-targets in the genome and the type of mutations (distance from PAM and clustering) to evaluate off-target cutting. The best sgRNA (lowest off-target score) in each exon are included in the library. Most genes have 3 or 4 sgRNAs targeting early exons. B) Individual sgRNAs are synthesized using array synthesis of ssDNAs and then PCR amplified as dsDNA. These dsDNAs are cloned into the lentiviral transfer plasmid after a U6 promoter; this vector also contains a EFS promoter driving Cas9 and puromycin resistance. The pooled library is packaged into lentiviral particles in HEK 293FT cells via co-transfection with pVSVg and psPAX2. To begin the screen, cells to be screened are infected at a MOI between 0.3 to 0.5 to ensure that each cell receives only 1 viral construct. In aspects of the invention, the MOI may be between 0.3 to 0.75. After 24 hours, cells are selected via puromycin so that only cells transduced with a CRISPR construct are preserved. C) Different sgRNA targeting the initial part of EGFP are cloned into the Cas9-2A-Puro lentiviral vector and packaged into virus. Distribution of EGFP fluorescence is shown for 293 Ts expressing EGFP after transduction with each EGFP-targeting sgRNA, a Cas9-only virus, or uninfected control cells. D) States NGS indel data on EGFP cells.

FIG. 24A-24F shows A) Timeline of Vemurafenib (PLX) resistance screen in A375 cells. B) Scatterplot of individual sgRNA abundances from biological replicates of DMSO treatment. C) Scatterplot of individual sgRNA abundances from biological replicates of PLX treatment. D) Boxplot showing the distribution of reads from different sgRNA. PLX has a statistically significant decrease in the average number of reads per sgRNA with an increase in the number in reads for the most abundant sgRNAs. E) Scatterplot of individual sgRNA abundances in PLX vs. DMSO treatment. F) Mapping of sgRNAs to genes and the calculating the median sgRNA enrichment value. By calculating an empirical distribution of p-values, a few gene knock outs display significant enrichment after PLX treatment, such as NF2, NF1, MED12, and MED15.

FIG. 25A-25C shows lentiviral delivery of Cas9 and sgRNA provides efficient depletion of target genes. (A) Lentiviral expression vector for Cas9 and sgRNA (lentiCRISPR). Puromycin selection marker (puro), psi packaging signal (psi+), rev response element (RRE), central polypurine tract (cPPT), and posttranscriptional regulatory element (WPRE). (B) Distribution of fluorescence from 293T-EGFP cells transduced by EGFP-targeting lentiCRISPR (sgRNAs 1-6, outlined peaks) and Cas9-only (green-shaded peak) vectors, and non-fluorescent 293T cells (grey shaded peak). (C) Distribution of fluorescence from 293T-EGFP cells transduced by EGFP-targeting shRNA (shRNAs 1-4, outlined peaks) and control shRNA (green-shaded peak) vectors, and non-fluorescent 293T cells (grey shaded peak).

FIG. 26A-26E shows GeCKO library design and application for genome-scale negative selection screening. (A) Design of sgRNA library for genome-scale knockout of coding sequences in human cells (supplementary discussion). (B), (C) Cumulative frequency of sgRNAs 3 and 14 days post transduction in A375 and hES cells respectively. Shift in the 14 day curve represents the depletion in a subset of sgRNAs. (D), (E) Five most significantly depleted gene sets in A375 cells (nominal p<10⁻⁵, FDR-corrected q<10⁻⁵) and HUES62 cells (nominal p<10⁻⁵, FDR-corrected q<10⁻³) identified by Gene Set Enrichment Analysis (GSEA).

FIG. 27A-27F shows GeCKO screen in A375 melanoma cells reveals genes whose loss confers vemurafenib (PLX) resistance. (A) Timeline of PLX resistance screen in A375 melanoma cells. (B) Growth of A375 cells when treated with DMSO or PLX over 14 days. (C) Boxplot showing the distribution of sgRNA frequencies at different time points, with and without PLX treatment (vehicle=DMSO). The box extends from the first to the third quartile with the whiskers denoting 1.5 times the interquartile range. Enrichment of specific sgRNAs: 7 days of PLX treatment, 1 sgRNA greater than 10-fold enrichment; 14 days of PLX treatment, 379 and 49 sgRNAs greater than 10-fold and 100-fold enrichment respectively. (D) Rank correlation of normalized sgRNA read count between biological replicates and treatment conditions. (E) Scatterplot showing enrichment of specific sgRNAs after PLX treatment. (F) Identification of top candidate genes using the RNAi Gene Enrichment Ranking (RIGER) p value analysis.

FIG. 28A-28E shows Comparison of GeCKO and shRNA screens and validation of neurofibromin 2 (NF2). (A) RIGER p values for the top 100 hits from GeCKO and shRNA screens for genes whose loss results in PLX resistance. Analysis using the Redundant siRNA Activity (RSA) algorithm shows a similar trend (fig. S9). (B) For the top 10 RIGER hits, the percent of unique sgRNAs (top) or shRNAs (bottom) targeting each gene that are in top 5% of all enriched sgRNAs or shRNAs. (C) Deep sequencing analysis of lentiCRISPR-mediated indel at the NF2 locus. (D) A375 cells transduced with NF2-targeting lentiCRISPR and shRNA vectors both show a decrease in NF2 protein levels. (E) Dose response curves for A375 cells transduced with individual NF2-targeting lentiCRISPR or shRNA vectors. Controls were EGFP-targeting lentiCRISPR or null hairpin shRNA vectors. Cells transduced with NF2-targeting lentiCRISPRs show a significant increase (F_(1, 8)=30.3, p<0.001, n=4 replicates) in the half maximal effective concentration (EC₅₀) whereas cells transduced with NF2-targeting shRNA vectors do not (F_(1,8)=0.47,p=0.51, n=4 replicates).

FIG. 29 shows design of sgRNAs to knock out EGFP. EGFP sequence (SEQ ID NO: 238) is shown with six different sgRNAs that were designed to target the coding sequence.

FIG. 30A-30B shows deep sequencing for indel analysis of EGFP locus after lentiCRISPR modification. (A) Deep-sequencing of genomic DNA from HEK293T-EGFP cells that were infected with EGFP-targeting lentiCRISPRs shows that most amplicons have insertion or deletion (indel) mutations. Genomic DNA was extracted from cells on day 11 post-infection. For each lentiCRISPR, 1-2×10⁴ reads were used for the analysis. (B) Distribution of types of indel mutations. lentiCRISPR transduction leads to both frameshift and in-frame indel mutations.

FIG. 31 shows Read coverage per sgRNA in a single experiment. Cumulative distribution of the number of reads per sgRNA in a single A375 experiment. The red line indicates that less than 4% of the sgRNAs are covered by less than 100 reads.

FIG. 32 shows Comparison of sgRNA representation between the plasmid pool to an early time point (day 7). Scatter plot of sgRNA representation (log₁₀ number of reads) between the plasmid pool before virus production to a cell population 7 days post infection. Red line indicates that less than 0.4% of sgRNA have undetectable representation (less than 10 reads).

FIG. 33A-33C shows Comparison of gene and gene category depletion between A375 melanoma and HUES62 human ES cells. (A) Scatter plot of gene enrichment/depletion as log₂ fold change of each gene between cells 14 days post-transduction and initial library plasmid in A375 melanoma cells and HUES62 hES cells. Gene enrichment/depletion was calculated using RIGER analysis of individual sgRNA depletion. Lower left quadrant contains genes depleted in both A375 and HUES62 cells. (B) Overlap between the top 1000 most depleted genes in each cell type. (C) Overlap between the top 100 most depleted Gene Ontology (GO) categories for each cell type as ranked by Gene Set Enrichment Analysis (GSEA) on the gene enrichment/depletion values.

FIG. 34 shows Comparison of different treatment conditions and biological replicates in the first A375 PLX screen. Each square in the lower left half of the matrix compares the normalized sgRNA read count between two biological samples. Sample labels for each axis are indicated on the diagonal. For example, the box on the second row from the bottom and third column from the right compares PLX day 7 (2) on the x-axis with PLX day 14 (1) on the y-axis. The Pearson correlation coefficient for comparison (i,j) can be found in box (j,i); for the example described in the previous sentence, the correlation coefficient is 0.81.

FIG. 35A-35B shows sgRNA and gene enrichment from the second A375 PLX screen. (A) Boxplot showing the distribution of reads from individual sgRNAs for the early timepoint, DMSO treated control, and PLX-4023 (PLX) treatment. The box extends from the first to the third quartile with the whiskers denoting 1.5 times the interquartile range. After 14 days of PLX treatment, while there is a decrease in the average number of reads per sgRNA, there is an increase in the number of reads for the most abundant sgRNAs. (B) Plot of the RIGER p value for genes enriched in PLX compared to vehicle control.

FIG. 36 shows Comparison of different treatment conditions and biological replicates in the infection replicate A375 screen. Each square in the lower left half of the matrix compares the normalized sgRNA read count between two biological samples. Sample labels for each axis are indicated on the diagonal. For example, the box on the second row from the bottom and third column from the right compares Vehicle day 14 (2) on the x-axis with PLX day 14 (1) on the y-axis. The Pearson correlation coefficient for comparison (i,j) can be found in box (j,i); for the example described in the previous sentence, the correlation coefficient is 0.75.

FIG. 37 shows Cumulative p value distribution for the top hits as determined by the Redundant siRNA Activity (RSA) algorithm. Lower p values signify a higher consistency of distinct reagents targeting the same genes. RSA calculates the significance of reagents concentrated near the top or bottom of an enrichment list through an iterative hypergeometric test

FIG. 38A-38F shows Array validation and comparison of the three highest-ranking genes using both CRISPR and shRNAs. Each panel shows cell survival data at different PLX doses as determined by CellTiter-Glo and protein quantification using western analysis. The gray line shows the mean of 2 control sgRNAs (targeting EGFP) or 2 control shRNAs (pLKO-nullT control vectors) and the colored line (blue for Cas9-sgRNAs, pink for shRNAs) shows the mean of all targeting reagents for the gene. n=4 replicates for dose response data. Shift in the dose response curve to the right of the control curve indicates greater resistance to PLX in the perturbed cell lines. (A), (B) Cas9-sgRNA and shRNA reagents respectively targeting NFL (C), (D) Cas9-sgRNA and shRNA reagents respectively targeting MED12. (E), (F) Cas9-sgRNA and shRNA reagents respectively targeting TADA2B gene.

FIG. 39A-39B shows Array validation of the two additional high-ranking genes. Each panel shows cell survival data at different PLX doses as determined by CellTiter-Glo and protein quantification using western analysis. The gray line shows the mean of 2 control sgRNAs that target EGFP and the blue line shows the mean of Cas9-sgRNAs targeted to the gene. Shift in the dose response curve displays the reduced sensitivity to PLX in the perturbed cell lines. (A) Cas9-sgRNAs targeting CUL3. (B) Cas9-sgRNAs targeting TADA1. Western analysis was not performed for TADA1 since neither of the two antibodies attempted yielded a band of the correct molecular weight.

FIG. 40 shows Measurements of allele modification frequencies in 25 sgRNAs targeting the seven highest-ranking genes in the A375 GeCKO screen. Bar plot shows the percentage of modified alleles determined by PCR followed by deep sequencing. Error bars representing Wilson intervals.

FIG. 41 shows Histograms of on-target indel sizes for NF2, MED12, and NFL Each subpanel shows the distribution of indel sizes for a single sgRNA at its intended genomic target locus. Each locus is PCR amplified and deep sequenced. Negative values indicate deletions and positive values indicate insertions.

FIG. 42 shows Measurements of on and off target allele modification frequencies for three sgRNAs targeting NF1. Each row represents a genomic locus consisting of a 20 bp sgRNA site (in black or gray letters) followed by a 3 bp PAM sequence (in light blue letters). Sequences in bold black letters indicate the genomic sequences that the GeCKO library sgRNAs were designed to target. Below each bold line are 3 to 5 predicted potential off target genomic sequences identified using the CRISPR design tool (available at the website tools.genome-engineering.org). Red nucleotides highlight the differences in these off target sequences from the on target site. Each locus (on and off target) was PCR amplified and then deep sequenced. Bars show the percentage of modified alleles 7 and 14 days post transduction with error bars representing Wilson intervals. FIG. 42 discloses SEQ ID NOS 239-254, respectively, in order of appearance.

FIG. 43 shows Measurements of on and off target allele modification frequencies for three sgRNAs targeting NF2. Each row represents a genomic locus consisting of a 20 bp sgRNA site (in black or gray letters) followed by a 3 bp PAM sequence (in light blue letters). Sequences in bold black letters indicate the genomic sequences that the GeCKO library sgRNAs were designed to target. Below each bold line are 3 to 5 predicted potential off target genomic sequences identified using the CRISPR design tool (available at the website tools.genome-engineering.org). Red nucleotides highlight the differences in these off target sequences from the on target site. Each locus (on and off target) was PCR amplified and then deep sequenced. Bars show the percentage of modified alleles 7 and 14 days post transduction with error bars representing Wilson intervals. FIG. 43 discloses SEQ ID NOS 255-275, respectively, in order of appearance.

FIG. 44 shows Measurements of on and off target allele modification frequencies for three sgRNAs targeting MED12. Each row represents a genomic locus consisting of a 20 bp sgRNA site (in black or gray letters) followed by a 3 bp PAM sequence (in light blue letters). Sequences in bold black letters indicate the genomic sequences that the GeCKO library sgRNAs were designed to target. Below each bold line are 3 to 5 predicted potential off target genomic sequences identified using the CRISPR design tool (available at the website tools.genome-engineering.org). Red nucleotides highlight the differences in these off target sequences from the on target site. Each locus (on and off target) was PCR amplified and then deep sequenced. Bars show the percentage of modified alleles 7 and 14 days post transduction with error bars representing Wilson intervals. FIG. 44 discloses SEQ ID NOS 276-284 and 284-298, respectively, in order of appearance.

FIG. 45A-45L shows Top 1000 depleted genes for both A375 and HUES62. Mean depletion for each gene is given as the log 2 ratio of Day 14 vs. Day 3 representation (mean over sgRNAs for the gene).

FIG. 46A-46E shows the plasmid map (SEQ ID NO: 299) & annotation key for LentiCRISPR (pXPR_001 available through Addgene)

FIG. 47A-47B shows New lentiviral CRISPR designs produce viruses with higher functional titer. (A) Lentiviral expression vector for Streptococcus pyogenes Cas9 and sgRNA in the improved one vector system (lentiCRISPR v2) and the two vector system (lentiCas9-Blast, lentiGuide-Puro). Psi packaging signal (psi+), rev response element (RRE), central polypurine tract (cPPT), elongation factor-1α short promoter (EFS), FLAG octapeptide tag (FLAG), 2A self-cleaving peptide (P2A), puromycin selection marker (puro), posttranscriptional regulatory element (WPRE), blasticidin selection marker (blast), and elongation factor-1α promoter (EF1a). (B) Relative functional viral titer of viruses made from lentiCRISPR v1, lentiCRISPR v2, and lentiGuide-Puro vector with a EGFP-targeting sgRNA (n=3 transductions). HEK293FT cells were transduced with serial dilutions of virus and, after 24 hours, selected using puromycin (1 ug/ml). Puromycin-resistant cells were measured after 4 days from the start of selection using the CellTiter-Glo (Promega) luciferase assay. Relative titers were calculated using viral volumes that yielded less than 20% puromycin-resistant cells in order to minimize the number of cells with multiple infections. Numbers above each bar indicate the size of the packaged virus for each construct.

FIG. 48A-48B shows Flow cytometry of HEK293T-EGFP 7 days after lentiCRISPR transduction. (A) Representative histograms of EGFP fluorescence from single transductions of HEK293T-EGFP cells with lentiCRISPR v1, lentiCRISPR v2, lentiGuide-Puro or no virus. For lentiGuide-Puro, HEK293T-EGFP cells had previously been transduced with lentiCas9-Blast. Twenty-four hours after transduction, cells were selected in puromycin and then analyzed by flow cytometry at 7 days after infection. (B) Percentage of EGFP positive cells (as given by gate drawn in panel A) per viral construct (error bars indicate s.e.m, n=3 biological replicate transductions).

FIG. 49A-49D shows the plasmid map (SEQ ID NO: 300) & annotation key for LentiCRISPR v2 available through Addgene.

FIG. 50A-50C shows the plasmid map (SEQ ID NO: 301) & annotation key for LentiCas9-Blast available through Addgene.

FIG. 51A-51C shows the plasmid map (SEQ ID NO: 302) & annotation key for lentiGuide-Puro available through Addgene.

The figures herein are for illustrative purposes only and are not necessarily drawn to scale.

DETAILED DESCRIPTION OF THE INVENTION

With respect to general information on CRISPR-Cas Systems: Reference is also made to U.S. provisional patent applications 61/736,527, 61/748,427, 61/791,409 and 61/835,931, filed on Dec. 12, 2012, Jan. 2, 2013, Mar. 15, 2013 and Jun. 17, 2013, respectively. Reference is also made to U.S. provisional applications 61/757,972 and 61/768,959, filed on Jan. 29, 2013 and Feb. 25, 2013, respectively. Reference is also made to U.S. provisional patent applications 61/835,931, 61/835,936, 61/836,127, 61/836,101, 61/836,080 and 61/835,973, each filed Jun. 17, 2013. Each of these applications, and all documents cited therein or during their prosecution (“appln cited documents”) and all documents cited or referenced in the appln cited documents, together with any instructions, descriptions, product specifications, and product sheets for any products mentioned therein or in any document therein and incorporated by reference herein, are hereby incorporated herein by reference in their entirety, and may be employed in the practice of the invention. All documents (e.g., these applications and the appln cited documents) are incorporated herein by reference to the same extent as if each individual document was specifically and individually indicated to be incorporated by reference.

Also with respect to general information on CRISPR-Cas Systems, mention is made of:

-   Multiplex genome engineering using CRISPR/Cas systems. Cong, L.,     Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D.,     Wu, X., Jiang, W., Marraffini, L. A., & Zhang, F. Science February     15; 339(6121):819-23 (2013); -   RNA-guided editing of bacterial genomes using CRISPR-Cas systems.     Jiang W., Bikard D., Cox D., Zhang F, Marraffini L A. Nat Biotechnol     March; 31(3):233-9 (2013); -   One-Step Generation of Mice Carrying Mutations in Multiple Genes by     CRISPR/Cas-Mediated Genome Engineering. Wang H., Yang H., Shivalila     C S., Dawlaty M M., Cheng AW., Zhang F., Jaenisch R. Cell May 9;     153(4):910-8 (2013); -   Optical control of mammalian endogenous transcription and epigenetic     states. Konermann S, Brigham M D, Trevino A E, Hsu P D, Heidenreich     M, Cong L, Platt R J, Scott D A, Church G M, Zhang F. Nature. 2013     Aug. 22; 500(7463):472-6. doi: 10.1038/Nature12466. Epub 2013 Aug.     23; -   Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing     Specificity. Ran, F A., Hsu, P D., Lin, C Y., Gootenberg, J S.,     Konermann, S., Trevino, A E., Scott, D A., Inoue, A., Matoba, S.,     Zhang, Y., & Zhang, F. Cell August 28. pii: S0092-8674(13)01015-5.     (2013); -   DNA targeting specificity of RNA guided Cas9 nucleases. Hsu, P.,     Scott, D., Weinstein, J., Ran, F A., Konermann, S., Agarwala, V.,     L1, Y., Fine, E., Wu, X., Shalem, O., Cradick, T J., Marraffini, L     A., Bao, G., & Zhang, F. Nat Biotechnol doi:10.1038/nbt.2647 (2013); -   Genome engineering using the CRISPR-Cas9 system. Ran, F A., Hsu, P     D., Wright, J., Agarwala, V., Scott, D A., Zhang, F. Nature     Protocols November; 8(11):2281-308. (2013); -   Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells. Shalem,     O., Sanjana, N E., Hartenian, E., Shi, X., Scott, D A., Mikkelson,     T., Heckl, D., Ebert, B L., Root, D E., Doench, J G., Zhang, F.     Science December 12. (2013). [Epub ahead of print]; -   Crystal structure of cas9 in complex with guide RNA and target DNA.     Nishimasu, H., Ran, F A., Hsu, P D., Konermann, S., Shehata, S I.,     Dohmae, N., Ishitani, R., Zhang, F., Nureki, O. Cell February 27.     (2014). 156(5):935-49; -   Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian     cells. Wu X., Scott D A., Kriz A J., Chiu A C., Hsu P D., Dadon D     B., Cheng A W., Trevino A E., Konermann S., Chen S., Jaenisch R.,     Zhang F., Sharp P A. Nat Biotechnol. (2014) Apr. 20. doi:     10.1038/nbt.2889, and -   Development and Applications of CRISPR-Cas9 for Genome Engineering,     Hsu et al, Cell 157, 1262-1278 (Jun. 5, 2014) (Hsu 2014),     each of which is incorporated herein by reference, and discussed     briefly below:     -   Cong et al. engineered type II CRISPR/Cas systems for use in         eukaryotic cells based on both Streptococcus thermophilus Cas9         and also Streptoccocus pyogenes Cas9 and demonstrated that Cas9         nucleases can be directed by short RNAs to induce precise         cleavage of DNA in human and mouse cells. Their study further         showed that Cas9 as converted into a nicking enzyme can be used         to facilitate homology-directed repair in eukaryotic cells with         minimal mutagenic activity. Additionally, their study         demonstrated that multiple guide sequences can be encoded into a         single CRISPR array to enable simultaneous editing of several at         endogenous genomic loci sites within the mammalian genome,         demonstrating easy programmability and wide applicability of the         RNA-guided nuclease technology. This ability to use RNA to         program sequence specific DNA cleavage in cells defined a new         class of genome engineering tools. These studies further showed         that other CRISPR loci are likely to be transplantable into         mammalian cells and can also mediate mammalian genome cleavage.         Importantly, it can be envisaged that several aspects of the         CRISPR/Cas system can be further improved to increase its         efficiency and versatility.     -   Jiang et al. used the clustered, regularly interspaced, short         palindromic repeats (CRISPR)-associated Cas9 endonuclease         complexed with dual-RNAs to introduce precise mutations in the         genomes of Streptococcus pneumoniae and Escherichia coli. The         approach relied on dual-RNA:Cas9-directed cleavage at the         targeted genomic site to kill unmutated cells and circumvents         the need for selectable markers or counter-selection systems.         The study reported reprogramming dual-RNA:Cas9 specificity by         changing the sequence of short CRISPR RNA (crRNA) to make         single- and multinucleotide changes carried on editing         templates. The study showed that simultaneous use of two crRNAs         enabled multiplex mutagenesis. Furthermore, when the approach         was used in combination with recombineering, in S. pneumoniae,         nearly 100% of cells that were recovered using the described         approach contained the desired mutation, and in E. coli, 65%         that were recovered contained the mutation.     -   Konermann et al. addressed the need in the art for versatile and         robust technologies that enable optical and chemical modulation         of DNA-binding domains based CRISPR Cas9 enzyme and also         Transcriptional Activator Like Effectors     -   As discussed in the present specification, the Cas9 nuclease         from the microbial CRISPR-Cas system is targeted to specific         genomic loci by a 20 nt guide sequence, which can tolerate         certain mismatches to the DNA target and thereby promote         undesired off-target mutagenesis. To address this, Ran et al.         described an approach that combined a Cas9 nickase mutant with         paired guide RNAs to introduce targeted double-strand breaks.         Because individual nicks in the genome are repaired with high         fidelity, simultaneous nicking via appropriately offset guide         RNAs is required for double-stranded breaks and extends the         number of specifically recognized bases for target cleavage. The         authors demonstrated that using paired nicking can reduce         off-target activity by 50- to 1,500-fold in cell lines and to         facilitate gene knockout in mouse zygotes without sacrificing         on-target cleavage efficiency. This versatile strategy enables a         wide variety of genome editing applications that require high         specificity.     -   Hsu et al. characterized SpCas9 targeting specificity in human         cells to inform the selection of target sites and avoid         off-target effects. The study evaluated >700 guide RNA variants         and SpCas9-induced indel mutation levels at >100 predicted         genomic off-target loci in 293T and 293FT cells. The authors         that SpCas9 tolerates mismatches between guide RNA and target         DNA at different positions in a sequence-dependent manner,         sensitive to the number, position and distribution of         mismatches. The authors further showed that SpCas9-mediated         cleavage is unaffected by DNA methylation and that the dosage of         SpCas9 and sgRNA can be titrated to minimize off-target         modification. Additionally, to facilitate mammalian genome         engineering applications, the authors reported providing a         web-based software tool to guide the selection and validation of         target sequences as well as off-target analyses.     -   Ran et al. described a set of tools for Cas9-mediated genome         editing via non-homologous end joining (NHEJ) or         homology-directed repair (HDR) in mammalian cells, as well as         generation of modified cell lines for downstream functional         studies. To minimize off-target cleavage, the authors further         described a double-nicking strategy using the Cas9 nickase         mutant with paired guide RNAs. The protocol provided by the         authors experimentally derived guidelines for the selection of         target sites, evaluation of cleavage efficiency and analysis of         off-target activity. The studies showed that beginning with         target design, gene modifications can be achieved within as         little as 1-2 weeks, and modified clonal cell lines can be         derived within 2-3 weeks.     -   Shalem et al. described a new way to interrogate gene function         on a genome-wide scale. Their studies showed that delivery of a         genome-scale CRISPR-Cas9 knockout (GeCKO) library targeted         18,080 genes with 64,751 unique guide sequences enabled both         negative and positive selection screening in human cells. First,         the authors showed use of the GeCKO library to identify genes         essential for cell viability in cancer and pluripotent stem         cells. Next, in a melanoma model, the authors screened for genes         whose loss is involved in resistance to vemurafenib, a         therapeutic that inhibits mutant protein kinase BRAF. Their         studies showed that the highest-ranking candidates included         previously validated genes NF1 and MED12 as well as novel hits         NF2, CUL3, TADA2B, and TADA1. The authors observed a high level         of consistency between independent guide RNAs targeting the same         gene and a high rate of hit confirmation, and thus demonstrated         the promise of genome-scale screening with Cas9.     -   Nishimasu et al. reported the crystal structure of Streptococcus         pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 A°         resolution. The structure revealed a bilobed architecture         composed of target recognition and nuclease lobes, accommodating         the sgRNA:DNA heteroduplex in a positively charged groove at         their interface. Whereas the recognition lobe is essential for         binding sgRNA and DNA, the nuclease lobe contains the HNH and         RuvC nuclease domains, which are properly positioned for         cleavage of the complementary and non-complementary strands of         the target DNA, respectively. The nuclease lobe also contains a         carboxyl-terminal domain responsible for the interaction with         the protospacer adjacent motif (PAM). This high-resolution         structure and accompanying functional analyses have revealed the         molecular mechanism of RNA-guided DNA targeting by Cas9, thus         paving the way for the rational design of new, versatile         genome-editing technologies.     -   Wu et al. mapped genome-wide binding sites of a catalytically         inactive Cas9 (dCas9) from Streptococcus pyogenes loaded with         single guide RNAs (sgRNAs) in mouse embryonic stem cells         (mESCs). The authors showed that each of the four sgRNAs tested         targets dCas9 to between tens and thousands of genomic sites,         frequently characterized by a 5-nucleotide seed region in the         sgRNA and an NGG protospacer adjacent motif (PAM). Chromatin         inaccessibility decreases dCas9 binding to other sites with         matching seed sequences; thus 70% of off-target sites are         associated with genes. The authors showed that targeted         sequencing of 295 dCas9 binding sites in mESCs transfected with         catalytically active Cas9 identified only one site mutated above         background levels. The authors proposed a two-state model for         Cas9 binding and cleavage, in which a seed match triggers         binding but extensive pairing with target DNA is required for         cleavage.     -   Hsu 2014 is a review article that discusses generally         CRISPR-Cas9 history from yogurt to genome editing, including         genetic screening of cells, that is in the information, data and         findings of the applications in the lineage of this         specification filed prior to Jun. 5, 2014. The general teachings         of Hsu 2014 do not involve the specific models, animals of the         instant specification.

Mention is also made of Cong et al, Supplementary Material . . . ”, Science 339(6121), pp 1-25); Jinek et al, Science 337(6096), 17 Aug. 2012, pp 816-821; Gasiunas et al, PNAS 19(39), 25 Sep. 2012, pp E2579-2586; Shalem et al, Science 343(6166), pp 84-87 (2014); Haft et al, PLOS Computational Biology, Public Library of Science, vol. 1, no. 6, pp 474-83 (2005); and Wiedenheft et al, Nature 482(7385), pp 331-338 (2012), each of which, in their entirety, is hereby incorporated herein by reference, without any admission that these or any document cited herein is indeed prior art as to the instant invention.

The terms “polynucleotide”, “nucleotide”, “nucleotide sequence”, “nucleic acid” and “oligonucleotide” are used interchangeably. They refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three dimensional structure, and may perform any function, known or unknown. The following are non limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, short interfering RNA (siRNA), short-hairpin RNA (shRNA), micro-RNA (miRNA), ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide may comprise one or more modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component.

As used herein the term “candidate gene” refers to a cellular, viral, episomal, microbial, protozoal, fungal, animal, plant, chloroplastic, or mitochondrial gene. This term also refers to a microbial or viral gene that is part of a naturally occurring microbial or viral genome in a microbially or virally infected cell. The microbial or viral genome can be extrachromosomal or integrated into the host chromosome. This term also encompasses endogenous and exogenous genes, as well as cellular genes that are identified as ESTs. Often, the candidate genes of the invention are those for which the biological function is unknown. An assay of choice is used to determine whether or not the gene is associated with a selected phenotype upon regulation of candidate gene expression with systems of the invention. If the biological function is known, typically the candidate gene acts as a control gene, or is used to determine if one or more additional genes are associated with the same phenotype, or is used to determine if the gene participates with other genes in a particular phenotype.

A “selected phenotype” refers to any phenotype, e.g., any observable characteristic or functional effect that can be measured in an assay such as changes in cell growth, proliferation, morphology, enzyme function, signal transduction, expression patterns, downstream expression patterns, reporter gene activation, hormone release, growth factor release, neurotransmitter release, ligand binding, apoptosis, and product formation. Such assays include, e.g., transformation assays, e.g., changes in proliferation, anchorage dependence, growth factor dependence, foci formation, growth in soft agar, tumor proliferation in nude mice, and tumor vascularization in nude mice; apoptosis assays, e.g., DNA laddering and cell death, expression of genes involved in apoptosis; signal transduction assays, e.g., changes in intracellular calcium, cAMP, cGMP, IP3, changes in hormone and neurotransmittor release; receptor assays, e.g., estrogen receptor and cell growth; growth factor assays, e.g., EPO, hypoxia and erythrocyte colony forming units assays; enzyme product assays, e.g., FAD-2 induced oil desaturation; transcription assays, e.g., reporter gene assays; and protein production assays, e.g., VEGF ELISAs. A candidate gene is “associated with” a selected phenotype if modulation of gene expression of the candidate gene causes a change in the selected phenotype

In aspects of the invention the terms “chimeric RNA”, “chimeric guide RNA”, “guide RNA”, “single guide RNA” and “synthetic guide RNA” are used interchangeably and refer to the polynucleotide sequence comprising the guide sequence, the tracr sequence and the tracr mate sequence. The term “guide sequence” refers to the about 20 bp sequence within the guide RNA that specifies the target site and may be used interchangeably with the terms “guide” or “spacer”. The term “tracr mate sequence” may also be used interchangeably with the term “direct repeat(s)”. An exemplary CRISPR-Cas system is illustrated in FIG. 1.

As used herein the term “wild type” is a term of the art understood by skilled persons and means the typical form of an organism, strain, gene or characteristic as it occurs in nature as distinguished from mutant or variant forms.

As used herein the term “variant” should be taken to mean the exhibition of qualities that have a pattern that deviates from what occurs in nature.

The terms “non-naturally occurring” or “engineered” are used interchangeably and indicate the involvement of the hand of man. The terms, when referring to nucleic acid molecules or polypeptides mean that the nucleic acid molecule or the polypeptide is at least substantially free from at least one other component with which they are naturally associated in nature and as found in nature.

“Complementarity” refers to the ability of a nucleic acid to form hydrogen bond(s) with another nucleic acid sequence by either traditional Watson-Crick base pairing or other non-traditional types. A percent complementarity indicates the percentage of residues in a nucleic acid molecule which can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary). “Perfectly complementary” means that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence. “Substantially complementary” as used herein refers to a degree of complementarity that is at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, or more nucleotides, or refers to two nucleic acids that hybridize under stringent conditions.

As used herein, “stringent conditions” for hybridization refers to conditions under which a nucleic acid having complementarity to a target sequence predominantly hybridizes with the target sequence, and substantially does not hybridize to non-target sequences. Stringent conditions are generally sequence-dependent, and vary depending on a number of factors. In general, the longer the sequence, the higher the temperature at which the sequence specifically hybridizes to its target sequence. Non-limiting examples of stringent conditions are described in detail in Tijssen (1993), Laboratory Techniques In Biochemistry And Molecular Biology-Hybridization With Nucleic Acid Probes Part I, Second Chapter “Overview of principles of hybridization and the strategy of nucleic acid probe assay”, Elsevier, N.Y.

“Hybridization” refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues. The hydrogen bonding may occur by Watson Crick base pairing, Hoogstein binding, or in any other sequence specific manner. The complex may comprise two strands forming a duplex structure, three or more strands forming a multi stranded complex, a single self hybridizing strand, or any combination of these. A hybridization reaction may constitute a step in a more extensive process, such as the initiation of PCR, or the cleavage of a polynucleotide by an enzyme. A sequence capable of hybridizing with a given sequence is referred to as the “complement” of the given sequence.

As used herein, “expression” refers to the process by which a polynucleotide is transcribed from a DNA template (such as into and mRNA or other RNA transcript) and/or the process by which a transcribed mRNA is subsequently translated into peptides, polypeptides, or proteins. Transcripts and encoded polypeptides may be collectively referred to as “gene product.” If the polynucleotide is derived from genomic DNA, expression may include splicing of the mRNA in a eukaryotic cell.

The terms “polypeptide”, “peptide” and “protein” are used interchangeably herein to refer to polymers of amino acids of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non amino acids. The terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component. As used herein the term “amino acid” includes natural and/or unnatural or synthetic amino acids, including glycine and both the D or L optical isomers, and amino acid analogs and peptidomimetics.

The terms “subject,” “individual,” and “patient” are used interchangeably herein to refer to a vertebrate, preferably a mammal, more preferably a human. Mammals include, but are not limited to, murines, simians, humans, farm animals, sport animals, and pets. Tissues, cells and their progeny of a biological entity obtained in vivo or cultured in vitro are also encompassed.

The terms “therapeutic agent”, “therapeutic capable agent” or “treatment agent” are used interchangeably and refer to a molecule or compound that confers some beneficial effect upon administration to a subject. The beneficial effect includes enablement of diagnostic determinations; amelioration of a disease, symptom, disorder, or pathological condition; reducing or preventing the onset of a disease, symptom, disorder or condition; and generally counteracting a disease, symptom, disorder or pathological condition.

As used herein, “treatment” or “treating,” or “palliating” or “ameliorating” are used interchangeably. These terms refer to an approach for obtaining beneficial or desired results including but not limited to a therapeutic benefit and/or a prophylactic benefit. By therapeutic benefit is meant any therapeutically relevant improvement in or effect on one or more diseases, conditions, or symptoms under treatment. For prophylactic benefit, the compositions may be administered to a subject at risk of developing a particular disease, condition, or symptom, or to a subject reporting one or more of the physiological symptoms of a disease, even though the disease, condition, or symptom may not have yet been manifested.

The term “effective amount” or “therapeutically effective amount” refers to the amount of an agent that is sufficient to effect beneficial or desired results. The therapeutically effective amount may vary depending upon one or more of: the subject and disease condition being treated, the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art. The term also applies to a dose that will provide an image for detection by any one of the imaging methods described herein. The specific dose may vary depending on one or more of: the particular agent chosen, the dosing regimen to be followed, whether it is administered in combination with other compounds, timing of administration, the tissue to be imaged, and the physical delivery system in which it is carried.

The practice of the present invention employs, unless otherwise indicated, conventional techniques of immunology, biochemistry, chemistry, molecular biology, microbiology, cell biology, genomics and recombinant DNA, which are within the skill of the art. See Sambrook, Fritsch and Maniatis, MOLECULAR CLONING: A LABORATORY MANUAL, 2nd edition (1989); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY (F. M. Ausubel, et al. eds., (1987)); the series METHODS IN ENZYMOLOGY (Academic Press, Inc.): PCR 2: A PRACTICAL APPROACH (M. J. MacPherson, B. D. Hames and G. R. Taylor eds. (1995)), Harlow and Lane, eds. (1988) ANTIBODIES, A LABORATORY MANUAL, and ANIMAL CELL CULTURE (R. I. Freshney, ed. (1987)).

Several aspects of the invention relate to vector systems comprising one or more vectors, or vectors as such. Vectors can be designed for expression of CRISPR transcripts (e.g. nucleic acid transcripts, proteins, or enzymes) in prokaryotic or eukaryotic cells. For example, CRISPR transcripts can be expressed in bacterial cells such as Escherichia coli, insect cells (using baculovirus expression vectors), yeast cells, or mammalian cells. Suitable host cells are discussed further in Goeddel, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990), the contents of which are incorporated herein by reference. Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example the lentiviral vectors encompassed in aspects of the invention may comprise a U6 RNA pol III promoter.

In general, and throughout this specification, the term “vector” refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. Vectors include, but are not limited to, nucleic acid molecules that are single-stranded, double-stranded, or partially double-stranded; nucleic acid molecules that comprise one or more free ends, no free ends (e.g. circular); nucleic acid molecules that comprise DNA, RNA, or both; and other varieties of polynucleotides known in the art. One type of vector is a “plasmid,” which refers to a circular double stranded DNA loop into which additional DNA segments can be inserted, such as by standard molecular cloning techniques. Another type of vector is a viral vector, wherein virally-derived DNA or RNA sequences are present in the vector for packaging into a virus (e.g. retroviruses, replication defective retroviruses, adenoviruses, replication defective adenoviruses, and adeno-associated viruses). Viral vectors also include polynucleotides carried by a virus for transfection into a host cell. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g. bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively-linked. Such vectors are referred to herein as “expression vectors.” Common expression vectors of utility in recombinant DNA techniques are often in the form of plasmids.

Recombinant expression vectors can comprise a nucleic acid of the invention in a form suitable for expression of the nucleic acid in a host cell, which means that the recombinant expression vectors include one or more regulatory elements, which may be selected on the basis of the host cells to be used for expression, that is operatively-linked to the nucleic acid sequence to be expressed. Within a recombinant expression vector, “operably linked” is intended to mean that the nucleotide sequence of interest is linked to the regulatory element(s) in a manner that allows for expression of the nucleotide sequence (e.g. in an in vitro transcription/translation system or in a host cell when the vector is introduced into the host cell).

The term “regulatory element” is intended to include promoters, enhancers, internal ribosomal entry sites (IRES), and other expression control elements (e.g. transcription termination signals, such as polyadenylation signals and poly-U sequences). Such regulatory elements are described, for example, in Goeddel, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990). Regulatory elements include those that direct constitutive expression of a nucleotide sequence in many types of host cell and those that direct expression of the nucleotide sequence only in certain host cells (e.g., tissue-specific regulatory sequences). A tissue-specific promoter may direct expression primarily in a desired tissue of interest, such as muscle, neuron, bone, skin, blood, specific organs (e.g. liver, pancreas), or particular cell types (e.g. lymphocytes). Regulatory elements may also direct expression in a temporal-dependent manner, such as in a cell-cycle dependent or developmental stage-dependent manner, which may or may not also be tissue or cell-type specific. In some embodiments, a vector comprises one or more pol III promoter (e.g. 1, 2, 3, 4, 5, or more pol III promoters), one or more pol II promoters (e.g. 1, 2, 3, 4, 5, or more pol II promoters), one or more pol I promoters (e.g. 1, 2, 3, 4, 5, or more pol I promoters), or combinations thereof. Examples of pol III promoters include, but are not limited to, U6 and H1 promoters. Examples of pol II promoters include, but are not limited to, the retroviral Rous sarcoma virus (RSV) LTR promoter (optionally with the RSV enhancer), the cytomegalovirus (CMV) promoter (optionally with the CMV enhancer) [see, e.g., Boshart et al, Cell, 41:521-530 (1985)], the SV40 promoter, the dihydrofolate reductase promoter, the β-actin promoter, the phosphoglycerol kinase (PGK) promoter, and the EF1a promoter. Also encompassed by the term “regulatory element” are enhancer elements, such as WPRE; CMV enhancers; the R-U5′ segment in LTR of HTLV-I (Mol. Cell. Biol., Vol. 8(1), p. 466-472, 1988); SV40 enhancer; and the intron sequence between exons 2 and 3 of rabbit β-globin (Proc. Natl. Acad. Sci. USA., Vol. 78(3), p. 1527-31, 1981). It will be appreciated by those skilled in the art that the design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression desired, etc. A vector can be introduced into host cells to thereby produce transcripts, proteins, or peptides, including fusion proteins or peptides, encoded by nucleic acids as described herein (e.g., clustered regularly interspersed short palindromic repeats (CRISPR) transcripts, proteins, enzymes, mutant forms thereof, fusion proteins thereof, etc.).

Some methods of the invention can include inducing expression. In some methods of the invention the organism or subject is a eukaryote (including mammal including human) or a non-human eukaryote or a non-human animal or a non-human mammal. In some methods of the invention the organism or subject is a plant. In some methods of the invention the organism or subject is a mammal or a non-human mammal. In some methods of the invention the organism or subject is algae. In some methods of the invention the viral vector is an AAV. In some methods of the invention the viral vector is a lentivirus-derived vector. In some methods of the invention the vector is an Agrobacterium Ti or Ri plasmid for use in plants. In some methods of the invention the CRISPR enzyme is a Cas9. In some methods of the invention the CRISPR enzyme copmprises one or more mutations in one of the catalytic domains. In some methods of the invention the CRISPR enzyme is a Cas9 nickase. In some methods of the invention the expression of the guide sequence is under the control of the T7 promoter that is driven by the expression of T7 polymerase. In some methods of the invention the expression of the guide sequence is under the control of a U6 promoter.

Two ways to package Cas9 coding nucleic acid molecules, e.g., DNA, into viral vectors to mediate genome modification in vivo are preferred: To achieve NHEJ-mediated gene knockout:

Single Virus Vector:

-   -   Vector containing two or more expression cassettes:     -   Promoter-Cas9 coding nucleic acid molecule-terminator     -   Promoter-gRNA 1-terminator     -   Promoter-gRNA2-terminator     -   Promoter-gRNA(N)-terminator (up to size limit of vector)

Double Virus Vector:

-   -   Vector 1 containing one expression cassette for driving the         expression of Cas9     -   Promoter-Cas9 coding nucleic acid molecule-terminator     -   Vector 2 containing one more expression cassettes for driving         the expression of one or more guideRNAs     -   Promoter-gRNA 1-terminator     -   Promoter-gRNA(N)-terminator (up to size limit of vector)         To mediate homology-directed repair:     -   In addition to the single and double virus vector approaches         described above, an additional vector is used to deliver a         homology-direct repair template.

Promoters used to drive Cas9 coding nucleic acid molecule expression are matched to the cell or organism into which the vector is to be expressed. In the case of a eukaryotic organism or cell, various Pol II promoters are available. In one aspect of the invention, the choice of promoter used to drive Cas9 coding nucleic acid molecule expression can include:

-   -   AAV ITR can serve as a promoter: this is advantageous for         eliminating the need for an additional promoter element (which         can take up space in the vector). The additional space freed up         can be used to drive the expression of additional elements         (gRNA, etc.). Also, ITR activity is relatively weaker, so can be         used to reduce toxicity due to over expression of Cas9;     -   For ubiquitous expression, can use promoters: CMV, CAG, CBh,         PGK, SV40, Ferritin heavy or light chains, etc.;     -   For cell-type specific expression, a variety of Pol II promoters         are available. Exemplary promoters can be selected from one or         more of the following nonlimiting list:         -   For brain expression, can use promoters: Synapsinl for all             neurons, CaMKllalpha for excitatory neurons, GAD67 or GAD65             or VGAT for GABAergic neurons, etc.;         -   For liver expression, can use Albumin promoter;         -   For lung expression, can use SP-B;         -   For endothelial cells, can use ICAM;         -   For hematopoietic cells can use IFNbeta or CD45; and         -   For Osteoblasts can use OG-2;

Promoter used to drive guide RNA can include:

Pol III promoters such as U6 or H1;

T7 promoter that is driven by the expression of T7 polymerase;

Use of Pol II promoter and intronic cassettes to express gRNA.

As to AAV, the AAV can be AAV1, AAV2, AAV5 or any combination thereof. One can select the AAV of the AAV with regard to the cells to be targeted; e.g., one can select AAV serotypes 1, 2, 5 or a hybrid or capsid AAV1, AAV2, AAV5 or any combination thereof for targeting brain or neuronal cells; and one can select AAV4 for targeting cardiac tissue. AAV8 is useful for delivery to the liver. The above promoters and vectors are preferred individually.

Advantageous vectors include vector systems derived from lentiviruses, adenoviruses and adeno-associated viruses, and types of such vectors can also be selected for targeting particular types of cells. In aspects on the invention the vectors may include but are not limited to packaged vectors. In other aspects of the invention a population of cells or host cells may be transduced with a vector with a low multiplicity of infection (MOI). As used herein the MOI is the ratio of infectious agents (e.g. phage or virus) to infection targets (e.g. cell). For example, when referring to a group of cells inoculated with infectious virus particles, the multiplicity of infection or MOI is the ratio of the number of infectious virus particles to the number of target cells present in a defined space (e.g. a well in a plate). In embodiments of the invention the cells are transduced with an MOI of 0.3-0.75 or 0.3-0.5; in preferred embodiments, the MOI has a value close to 0.4 and in more preferred embodiments the MOI is 0.3. In aspects of the invention the vector library of the invention may be applied to a well of a plate to attain a transduction efficiency of at least 20%, 30%, 40%, 50%, 60%, 70%, or 80%. In a preferred embodiment the transduction efficiency is approximately 30% wherein it may be approximately 370-400 cells per lentiCRISPR construct. In a more preferred embodiment, it may be 400 cells per lentiCRISPR construct.

Vectors may be introduced and propagated in a prokaryote. In some embodiments, a prokaryote is used to amplify copies of a vector to be introduced into a eukaryotic cell or as an intermediate vector in the production of a vector to be introduced into a eukaryotic cell (e.g. amplifying a plasmid as part of a viral vector packaging system). In some embodiments, a prokaryote is used to amplify copies of a vector and express one or more nucleic acids, such as to provide a source of one or more proteins for delivery to a host cell or host organism. Expression of proteins in prokaryotes is most often carried out in Escherichia coli with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Fusion vectors add a number of amino acids to a protein encoded therein, such as to the amino terminus of the recombinant protein. Such fusion vectors may serve one or more purposes, such as: (i) to increase expression of recombinant protein; (ii) to increase the solubility of the recombinant protein; and (iii) to aid in the purification of the recombinant protein by acting as a ligand in affinity purification. Often, in fusion expression vectors, a proteolytic cleavage site is introduced at the junction of the fusion moiety and the recombinant protein to enable separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Such enzymes, and their cognate recognition sequences, include Factor Xa, thrombin and enterokinase. Example fusion expression vectors include pGEX (Pharmacia Biotech Inc; Smith and Johnson, 1988. Gene 67: 31-40), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia, Piscataway, N.J.) that fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the target recombinant protein.

Examples of suitable inducible non-fusion E. coli expression vectors include pTrc (Amrann et al., (1988) Gene 69:301-315) and pET 11d (Studier et al., GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990) 60-89).

In some embodiments, a vector is a yeast expression vector. Examples of vectors for expression in yeast Saccharomyces cerivisae include pYepSec1 (Baldari, et al., 1987. EMBO J. 6: 229-234), pMFa (Kuijan and Herskowitz, 1982. Cell 30: 933-943), pJRY88 (Schultz et al., 1987. Gene 54: 113-123), pYES2 (Invitrogen Corporation, San Diego, Calif.), and picZ (InVitrogen Corp, San Diego, Calif.).

In some embodiments, a vector drives protein expression in insect cells using baculovirus expression vectors. Baculovirus vectors available for expression of proteins in cultured insect cells (e.g., SF9 cells) include the pAc series (Smith, et al., 1983. Mol. Cell. Biol. 3: 2156-2165) and the pVL series (Lucklow and Summers, 1989. Virology 170: 31-39).

In some embodiments, a vector is capable of driving expression of one or more sequences in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include pCDM8 (Seed, 1987. Nature 329: 840) and pMT2PC (Kaufman, et al., 1987. EMBO J. 6: 187-195). When used in mammalian cells, the expression vector's control functions are typically provided by one or more regulatory elements. For example, commonly used promoters are derived from polyoma, adenovirus 2, cytomegalovirus, simian virus 40, and others disclosed herein and known in the art. For other suitable expression systems for both prokaryotic and eukaryotic cells see, e.g., Chapters 16 and 17 of Sambrook, et al., MOLECULAR CLONING: A LABORATORY MANUAL. 2nd ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989.

In some embodiments, the recombinant mammalian expression vector is capable of directing expression of the nucleic acid preferentially in a particular cell type (e.g., tissue-specific regulatory elements are used to express the nucleic acid). Tissue-specific regulatory elements are known in the art. Non-limiting examples of suitable tissue-specific promoters include the albumin promoter (liver-specific; Pinkert, et al., 1987. Genes Dev. 1: 268-277), lymphoid-specific promoters (Calame and Eaton, 1988. Adv. Immunol. 43: 235-275), in particular promoters of T cell receptors (Winoto and Baltimore, 1989. EMBO J. 8: 729-733) and immunoglobulins (Baneiji, et al., 1983. Cell 33: 729-740; Queen and Baltimore, 1983. Cell 33: 741-748), neuron-specific promoters (e.g., the neurofilament promoter; Byrne and Ruddle, 1989. Proc. Natl. Acad. Sci. USA 86: 5473-5477), pancreas-specific promoters (Edlund, et al., 1985. Science 230: 912-916), and mammary gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No. 4,873,316 and European Application Publication No. 264,166). Developmentally-regulated promoters are also encompassed, e.g., the murine hox promoters (Kessel and Gruss, 1990. Science 249: 374-379) and the a-fetoprotein promoter (Campes and Tilghman, 1989. Genes Dev. 3: 537-546).

In some embodiments, a regulatory element is operably linked to one or more elements of a CRISPR system so as to drive expression of the one or more elements of the CRISPR system. In general, CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats), also known as SPIDRs (SPacer Interspersed Direct Repeats), constitute a family of DNA loci that are usually specific to a particular bacterial species. The CRISPR locus comprises a distinct class of interspersed short sequence repeats (SSRs) that were recognized in E. coli (Ishino et al., J. Bacteriol., 169:5429-5433 [1987]; and Nakata et al., J. Bacteriol., 171:3553-3556 [1989]), and associated genes. Similar interspersed SSRs have been identified in Haloferax mediterranei, Streptococcus pyogenes, Anabaena, and Mycobacterium tuberculosis (See, Groenen et al., Mol. Microbiol., 10:1057-1065 [1993]; Hoe et al., Emerg. Infect. Dis., 5:254-263 [1999]; Masepohl et al., Biochim. Biophys. Acta 1307:26-30 [1996]; and Mojica et al., Mol. Microbiol., 17:85-93 [1995]). The CRISPR loci typically differ from other SSRs by the structure of the repeats, which have been termed short regularly spaced repeats (SRSRs) (Janssen et al., OMICS J. Integ. Biol., 6:23-33 [2002]; and Mojica et al., Mol. Microbiol., 36:244-246 [2000]). In general, the repeats are short elements that occur in clusters that are regularly spaced by unique intervening sequences with a substantially constant length (Mojica et al., [2000], supra). Although the repeat sequences are highly conserved between strains, the number of interspersed repeats and the sequences of the spacer regions typically differ from strain to strain (van Embden et al., J. Bacteriol., 182:2393-2401 [2000]). CRISPR loci have been identified in more than 40 prokaryotes (See e.g., Jansen et al., Mol. Microbiol., 43:1565-1575 [2002]; and Mojica et al., [2005]) including, but not limited to Aeropyrum, Pyrobaculum, Sulfolobus, Archaeoglobus, Halocarcula, Methanobacterium, Methanococcus, Methanosarcina, Methanopyrus, Pyrococcus, Picrophilus, Thermoplasma, Corynebacterium, Mycobacterium, Streptomyces, Aquifex, Porphyromonas, Chlorobium, Thermus, Bacillus, Listeria, Staphylococcus, Clostridium, Thermoanaerobacter, Mycoplasma, Fusobacterium, Azarcus, Chromobacterium, Neisseria, Nitrosomonas, Desulfovibrio, Geobacter, Myxococcus, Campylobacter, Wolinella, Acinetobacter, Envinia, Escherichia, Legionella, Methylococcus, Pasteurella, Photobacterium, Salmonella, Xanthomonas, Yersinia, Treponema, and Thermotoga.

In aspects of the invention functional genomics screens allow for discovery of novel human and mammalian therapeutic applications, including the discovery of novel drugs, for, e.g., treatment of genetic diseases, cancer, fungal, protozoal, bacterial, and viral infection, ischemia, vascular disease, arthritis, immunological disorders, etc. As used herein assay systems may be used for a readout of cell state or changes in phenotype include, e.g., transformation assays, e.g., changes in proliferation, anchorage dependence, growth factor dependence, foci formation, growth in soft agar, tumor proliferation in nude mice, and tumor vascularization in nude mice; apoptosis assays, e.g., DNA laddering and cell death, expression of genes involved in apoptosis; signal transduction assays, e.g., changes in intracellular calcium, cAMP, cGMP, IP3, changes in hormone and neurotransmittor release; receptor assays, e.g., estrogen receptor and cell growth; growth factor assays, e.g., EPO, hypoxia and erythrocyte colony forming units assays; enzyme product assays, e.g., FAD-2 induced oil desaturation; transcription assays, e.g., reporter gene assays; and protein production assays, e.g., VEGF ELISAs.

Aspects of the invention relate to modulation of gene expression and modulation can be assayed by determining any parameter that is indirectly or directly affected by the expression of the target candidate gene. Such parameters include, e.g., changes in RNA or protein levels, changes in protein activity, changes in product levels, changes in downstream gene expression, changes in reporter gene transcription (luciferase, CAT, beta-galactosidase, beta-glucuronidase, GFP (see, e.g., Mistili & Spector, Nature Biotechnology 15:961-964 (1997)); changes in signal transduction, phosphorylation and dephosphorylation, receptor-ligand interactions, second messenger concentrations (e.g., cGMP, cAMP, IP3, and Ca²⁺), cell growth, and neovascularization, etc., as described herein. These assays can be in vitro, in vivo, and ex vivo. Such functional effects can be measured by any means known to those skilled in the art, e.g., measurement of RNA or protein levels, measurement of RNA stability, identification of downstream or reporter gene expression, e.g., via chemiluminescence, fluorescence, calorimetric reactions, antibody binding, inducible markers, ligand binding assays; changes in intracellular second messengers such as cGMP and inositol triphosphate (IP3); changes in intracellular calcium levels; cytokine release, and the like, as described herein.

Several methods of DNA extraction and analysis are encompassed in the methods of the invention. As used herein “deep sequencing” indicates that the depth of the process is many times larger than the length of the sequence under study. Deep sequencing is encompassed in next generation sequencing methods which include but are not limited to single molecule real-time sequencing (Pacific Bio), Ion semiconductor (Ion torrent sequencing), Pyrosequencing (454), Sequencing by synthesis (Illumina), Sequencing by ligations (SOLiD sequencing) and Chain termination (Sanger sequencing).

To determine the level of gene expression modulated by the CRISPR-Cas system, cells contacted with the CRISPR-Cas system are compared to control cells, e.g., without the CRISPR-Cas system or with a non-specific CRISPR-Cas system, to examine the extent of inhibition or activation. Control samples may be assigned a relative gene expression activity value of 100%. Modulation/inhibition of gene expression is achieved when the gene expression activity value relative to the control is about 80%, preferably 50% (i.e., 0.5 times the activity of the control), more preferably 25%, more preferably 5-0%. Modulation/activation of gene expression is achieved when the gene expression activity value relative to the control is 110%, more preferably 150% (i.e., 1.5 times the activity of the control), more preferably 200-500%, more preferably 1000-2000% or more.

In general, “CRISPR system” or the “CRISPR-Cas system” refers collectively to transcripts and other elements involved in the expression of or directing the activity of CRISPR-associated (“Cas”) genes, including sequences encoding a Cas gene, a tracr (trans-activating CRISPR) sequence (e.g. tracrRNA or an active partial tracrRNA), a tracr-mate sequence (encompassing a “direct repeat” and a tracrRNA-processed partial direct repeat in the context of an endogenous CRISPR system), a guide sequence (also referred to as a “spacer” in the context of an endogenous CRISPR system), or other sequences and transcripts from a CRISPR locus. In some embodiments, one or more elements of a CRISPR system is derived from a type I, type II, or type III CRISPR system. In some embodiments, one or more elements of a CRISPR system is derived from a particular organism comprising an endogenous CRISPR system, such as Streptococcus pyogenes. In general, a CRISPR system is characterized by elements that promote the formation of a CRISPR complex at the site of a target sequence (also referred to as a protospacer in the context of an endogenous CRISPR system). In the context of formation of a CRISPR complex, “target sequence” refers to a sequence to which a guide sequence is designed to have complementarity, where hybridization between a target sequence and a guide sequence promotes the formation of a CRISPR complex. Full complementarity is not necessarily required, provided there is sufficient complementarity to cause hybridization and promote formation of a CRISPR complex. A target sequence may comprise any polynucleotide, such as DNA or RNA polynucleotides. In some embodiments, a target sequence is located in the nucleus or cytoplasm of a cell. In some embodiments, the target sequence may be within an organelle of a eukaryotic cell, for example, mitochondrion or chloroplast. A sequence or template that may be used for recombination into the targeted locus comprising the target sequences is referred to as an “editing template” or “editing polynucleotide” or “editing sequence”. In aspects of the invention, an exogenous template polynucleotide may be referred to as an editing template. In an aspect of the invention the recombination is homologous recombination.

Typically, in the context of an endogenous CRISPR system, formation of a CRISPR complex (comprising a guide sequence hybridized to a target sequence and complexed with one or more Cas proteins) results in cleavage of one or both strands in or near (e.g. within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or more base pairs from) the target sequence. Without wishing to be bound by theory, the tracr sequence, which may comprise or consist of all or a portion of a wild-type tracr sequence (e.g. about or more than about 20, 26, 32, 45, 48, 54, 63, 67, 85, or more nucleotides of a wild-type tracr sequence), may also form part of a CRISPR complex, such as by hybridization along at least a portion of the tracr sequence to all or a portion of a tracr mate sequence that is operably linked to the guide sequence. In some embodiments, the tracr sequence has sufficient complementarity to a tracr mate sequence to hybridize and participate in formation of a CRISPR complex. As with the target sequence, it is believed that complete complementarity is not needed, provided there is sufficient to be functional. In some embodiments, the tracr sequence has at least 50%, 60%, 70%, 80%, 90%, 95% or 99% of sequence complementarity along the length of the tracr mate sequence when optimally aligned. In some embodiments, one or more vectors driving expression of one or more elements of a CRISPR system are introduced into a host cell such that expression of the elements of the CRISPR system direct formation of a CRISPR complex at one or more target sites. For example, a Cas enzyme, a guide sequence linked to a tracr-mate sequence, and a tracr sequence could each be operably linked to separate regulatory elements on separate vectors. Alternatively, two or more of the elements expressed from the same or different regulatory elements, may be combined in a single vector, with one or more additional vectors providing any components of the CRISPR system not included in the first vector. CRISPR system elements that are combined in a single vector may be arranged in any suitable orientation, such as one element located 5′ with respect to (“upstream” of) or 3′ with respect to (“downstream” of) a second element. The coding sequence of one element may be located on the same or opposite strand of the coding sequence of a second element, and oriented in the same or opposite direction. In some embodiments, a single promoter drives expression of a transcript encoding a CRISPR enzyme and one or more of the guide sequence, tracr mate sequence (optionally operably linked to the guide sequence), and a tracr sequence embedded within one or more intron sequences (e.g. each in a different intron, two or more in at least one intron, or all in a single intron). In some embodiments, the CRISPR enzyme, guide sequence, tracr mate sequence, and tracr sequence are operably linked to and expressed from the same promoter.

In some embodiments, a vector comprises one or more insertion sites, such as a restriction endonuclease recognition sequence (also referred to as a “cloning site”). In some embodiments, one or more insertion sites (e.g. about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more insertion sites) are located upstream and/or downstream of one or more sequence elements of one or more vectors. In some embodiments, a vector comprises an insertion site upstream of a tracr mate sequence, and optionally downstream of a regulatory element operably linked to the tracr mate sequence, such that following insertion of a guide sequence into the insertion site and upon expression the guide sequence directs sequence-specific binding of a CRISPR complex to a target sequence in a eukaryotic cell. In some embodiments, a vector comprises two or more insertion sites, each insertion site being located between two tracr mate sequences so as to allow insertion of a guide sequence at each site. In such an arrangement, the two or more guide sequences may comprise two or more copies of a single guide sequence, two or more different guide sequences, or combinations of these. When multiple different guide sequences are used, a single expression construct may be used to target CRISPR activity to multiple different, corresponding target sequences within a cell. For example, a single vector may comprise about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or more guide sequences. In some embodiments, about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more such guide-sequence-containing vectors may be provided, and optionally delivered to a cell.

In some embodiments, a vector comprises a regulatory element operably linked to an enzyme-coding sequence encoding a CRISPR enzyme, such as a Cas protein. Non-limiting examples of Cas proteins include Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cash, Cas7, Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3, Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, homologs thereof, or modified versions thereof. These enzymes are known; for example, the amino acid sequence of S. pyogenes Cas9 protein may be found in the SwissProt database under accession number Q99ZW2. In some embodiments, the unmodified CRISPR enzyme has DNA cleavage activity, such as Cas9. In some embodiments the CRISPR enzyme is Cas9, and may be Cas9 from S. pyogenes or S. pneumoniae. In some embodiments, the CRISPR enzyme directs cleavage of one or both strands at the location of a target sequence, such as within the target sequence and/or within the complement of the target sequence. In some embodiments, the CRISPR enzyme directs cleavage of one or both strands within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more base pairs from the first or last nucleotide of a target sequence. In some embodiments, a vector encodes a CRISPR enzyme that is mutated to with respect to a corresponding wild-type enzyme such that the mutated CRISPR enzyme lacks the ability to cleave one or both strands of a target polynucleotide containing a target sequence. For example, an aspartate-to-alanine substitution (D10A) in the RuvC I catalytic domain of Cas9 from S. pyogenes converts Cas9 from a nuclease that cleaves both strands to a nickase (cleaves a single strand). Other examples of mutations that render Cas9 a nickase include, without limitation, H840A, N854A, and N863A. In aspects of the invention, nickases may be used for genome editing via homologous recombination, For example, FIG. 21 shows genome editing via homologous recombination. FIG. 21 (a) shows the schematic of SpCas9 nickase, with D10A mutation in the RuvC I catalytic domain. (b) Schematic representing homologous recombination (HR) at the human EMX1 locus using either sense or antisense single stranded oligonucleotides as repair templates. (c) Sequence of region modified by HR. d, SURVEYOR assay for wildtype (wt) and nickase (D10A) SpCas9-mediated indels at the EMX1 target 1 locus (n=3). Arrows indicate positions of expected fragment sizes.

In some embodiments, a Cas9 nickase may be used in combination with one or more guide sequence(s), e.g., two guide sequences, which target respectively sense and antisense strands of the DNA duplex of the gene target. This combination allows both strands to be nicked and used to induce NHEJ. Applicants have demonstrated (data not shown) the efficacy of two nickase targets (i.e., sgRNAs targeted at the same location but to different strands of DNA) in inducing mutagenic NHEJ. A single nickase (Cas9-D10A with a single sgRNA) is unable to induce NHEJ and create indels but Applicants have shown that double nickase (Cas9-D10A and two sgRNAs targeted to different strands at the same location) can do so in human embryonic stem cells (hESCs). The efficiency is about 50% of nuclease (i.e., regular Cas9 without D10 mutation) in hESCs.

As a further example, two or more catalytic domains of Cas9 (RuvC I, RuvC II, and RuvC III) may be mutated to produce a mutated Cas9 substantially lacking all DNA cleavage activity. In some embodiments, a D10A mutation is combined with one or more of H840A, N854A, or N863A mutations to produce a Cas9 enzyme substantially lacking all DNA cleavage activity. In some embodiments, a CRISPR enzyme is considered to substantially lack all DNA cleavage activity when the DNA cleavage activity of the mutated enzyme is less than about 25%, 10%, 5%, 1%, 0.1%, 0.01%, or lower with respect to its non-mutated form. Other mutations may be useful; where the Cas9 or other CRISPR enzyme is from a species other than S. pyogenes, mutations in corresponding amino acids may be made to achieve similar effects.

In some embodiments, an enzyme coding sequence encoding a CRISPR enzyme is codon optimized for expression in particular cells, such as eukaryotic cells. The eukaryotic cells may be those of or derived from a particular organism, such as a mammal, including but not limited to human, mouse, rat, rabbit, dog, or non-human primate. In general, codon optimization refers to a process of modifying a nucleic acid sequence for enhanced expression in the host cells of interest by replacing at least one codon (e.g. about or more than about 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more codons) of the native sequence with codons that are more frequently or most frequently used in the genes of that host cell while maintaining the native amino acid sequence. Various species exhibit particular bias for certain codons of a particular amino acid. Codon bias (differences in codon usage between organisms) often correlates with the efficiency of translation of messenger RNA (mRNA), which is in turn believed to be dependent on, among other things, the properties of the codons being translated and the availability of particular transfer RNA (tRNA) molecules. The predominance of selected tRNAs in a cell is generally a reflection of the codons used most frequently in peptide synthesis. Accordingly, genes can be tailored for optimal gene expression in a given organism based on codon optimization. Codon usage tables are readily available, for example, at the “Codon Usage Database”, and these tables can be adapted in a number of ways. See Nakamura, Y., et al. “Codon usage tabulated from the international DNA sequence databases: status for the year 2000” Nucl. Acids Res. 28:292 (2000). Computer algorithms for codon optimizing a particular sequence for expression in a particular host cell are also available, such as Gene Forge (Aptagen; Jacobus, Pa.), are also available. In some embodiments, one or more codons (e.g. 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more, or all codons) in a sequence encoding a CRISPR enzyme correspond to the most frequently used codon for a particular amino acid.

In general, a guide sequence is any polynucleotide sequence having sufficient complementarity with a target polynucleotide sequence to hybridize with the target sequence and direct sequence-specific binding of a CRISPR complex to the target sequence. In some embodiments, the degree of complementarity between a guide sequence and its corresponding target sequence, when optimally aligned using a suitable alignment algorithm, is about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%, 99%, or more. Optimal alignment may be determined with the use of any suitable algorithm for aligning sequences, non-limiting example of which include the Smith-Waterman algorithm, the Needleman-Wunsch algorithm, algorithms based on the Burrows-Wheeler Transform (e.g. the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign (Novocraft Technologies, ELAND (Illumina, San Diego, Calif.), SOAP (available at soap.genomics.org.cn), and Maq (available at maq.sourceforge.net). In some embodiments, a guide sequence is about or more than about 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in length. In some embodiments, a guide sequence is less than about 75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in length. The ability of a guide sequence to direct sequence-specific binding of a CRISPR complex to a target sequence may be assessed by any suitable assay. For example, the components of a CRISPR system sufficient to form a CRISPR complex, including the guide sequence to be tested, may be provided to a host cell having the corresponding target sequence, such as by transfection with vectors encoding the components of the CRISPR sequence, followed by an assessment of preferential cleavage within the target sequence, such as by Surveyor assay as described herein. Similarly, cleavage of a target polynucleotide sequence may be evaluated in a test tube by providing the target sequence, components of a CRISPR complex, including the guide sequence to be tested and a control guide sequence different from the test guide sequence, and comparing binding or rate of cleavage at the target sequence between the test and control guide sequence reactions. Other assays are possible, and will occur to those skilled in the art.

A guide sequence may be selected to target any target sequence. In some embodiments, the target sequence is a sequence within a genome of a cell. Exemplary target sequences include those that are unique in the target genome. For example, for the S. pyogenes Cas9, a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXGG (SEQ ID NO: 303) where NNNNNNNNNNNNXGG (SEQ ID NO: 304) (N is A, G, T, or C; and X can be anything) has a single occurrence in the genome. A unique target sequence in a genome may include an S. pyogenes Cas9 target site of the form MMMMMMMMMNNNNNNNNNNNXGG (SEQ ID NO: 305) where NNNNNNNNNNNXGG (SEQ ID NO: 306) (N is A, G, T, or C; and X can be anything) has a single occurrence in the genome. For the S. thermophilus CRISPR1 Cas9, a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXXAGAAW (SEQ ID NO: 1) where NNNNNNNNNNNNXXAGAAW (N is A, G, T, or C; X can be anything; and W is A or T) (SEQ ID NO: 2) has a single occurrence in the genome. A unique target sequence in a genome may include an S. thermophilus CRISPR1 Cas9 target site of the form MMMMMMMMMNNNNNNNNNNNXXAGAAW (SEQ ID NO: 3) where NNNNNNNNNNNXXAGAAW (N is A, G, T, or C; X can be anything; and W is A or T) (SEQ ID NO: 4) has a single occurrence in the genome. For the S. pyogenes Cas9, a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXGGXG (SEQ ID NO: 307) where NNNNNNNNNNNNNNNNNNNNNNNNXGGXG (SEQ ID NO: 308) (N is A, G, T, or C; and X can be anything) has a single occurrence in the genome. A unique target sequence in a genome may include an S. pyogenes Cas9 target site of the form MMMMMMMMMNNNNNNNNNNNXGGXG (SEQ ID NO: 309) where NNNNNNNNNNNXGGXG (SEQ ID NO: 310) (N is A, G, T, or C; and X can be anything) has a single occurrence in the genome. In each of these sequences “M” may be A, G, T, or C, and need not be considered in identifying a sequence as unique.

In some embodiments, a guide sequence is selected to reduce the degree of secondary structure within the guide sequence. Secondary structure may be determined by any suitable polynucleotide folding algorithm. Some programs are based on calculating the minimal Gibbs free energy. An example of one such algorithm is mFold, as described by Zuker and Stiegler (Nucleic Acids Res. 9 (1981), 133-148). Another example folding algorithm is the online webserver RNAfold, developed at Institute for Theoretical Chemistry at the University of Vienna, using the centroid structure prediction algorithm (see e.g. A.R. Gruber et al., 2008, Cell 106(1): 23-24; and P A Carr and G M Church, 2009, Nature Biotechnology 27(12): 1151-62). Further algorithms may be found in U.S. application Ser. No. 61/836,080 (attorney docket 44790.11.2022; Broad Reference BI-2013/004A); incorporated herein by reference.

In general, a tracr mate sequence includes any sequence that has sufficient complementarity with a tracr sequence to promote one or more of: (1) excision of a guide sequence flanked by tracr mate sequences in a cell containing the corresponding tracr sequence; and (2) formation of a CRISPR complex at a target sequence, wherein the CRISPR complex comprises the tracr mate sequence hybridized to the tracr sequence. In general, degree of complementarity is with reference to the optimal alignment of the tracr mate sequence and tracr sequence, along the length of the shorter of the two sequences. Optimal alignment may be determined by any suitable alignment algorithm, and may further account for secondary structures, such as self-complementarity within either the tracr sequence or tracr mate sequence.

In some embodiments, the degree of complementarity between the tracr sequence and tracr mate sequence along the length of the shorter of the two when optimally aligned is about or more than about 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97.5%, 99%, or higher. Example illustrations of optimal alignment between a tracr sequence and a tracr mate sequence are provided in FIGS. 10B and 11B. In some embodiments, the tracr sequence is about or more than about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 40, 50, or more nucleotides in length. In some embodiments, the tracr sequence and tracr mate sequence are contained within a single transcript, such that hybridization between the two produces a transcript having a secondary structure, such as a hairpin. Preferred loop forming sequences for use in hairpin structures are four nucleotides in length, and most preferably have the sequence GAAA. However, longer or shorter loop sequences may be used, as may alternative sequences. The sequences preferably include a nucleotide triplet (for example, AAA), and an additional nucleotide (for example C or G). Examples of loop forming sequences include CAAA and AAAG. In an embodiment of the invention, the transcript or transcribed polynucleotide sequence has at least two or more hairpins. In preferred embodiments, the transcript has two, three, four or five hairpins. In a further embodiment of the invention, the transcript has at most five hairpins. In some embodiments, the single transcript further includes a transcription termination sequence; preferably this is a polyT sequence, for example six T nucleotides. Further non-limiting examples of single polynucleotides comprising a guide sequence, a tracr mate sequence, and a tracr sequence are as follows (listed 5′ to 3′), where “N” represents a base of a guide sequence, the first block of lower case letters represent the tracr mate sequence, and the second block of lower case letters represent the tracr sequence, and the final poly-T sequence represents the transcription terminator: (1) NNNNNNNNNN NNNNNNNNNN gtttttgtac tctcaagatt taGAAAtaaa tcttgcagaa gctacaaaga taaggcttca tgccgaaatc aacaccctgt cattttatgg cagggtgttt tcgttattta aTTTTTT (SEQ ID NO: 5); (2) NNNNNNNNNN NNNNNNNNNN gtttttgtac tctcaGAAAt gcagaagcta caaagataag gcttcatgcc gaaatcaaca ccctgtcatt ttatggcagg gtgttttcgt tatttaaTTT TTT (SEQ ID NO: 6); (3) NNNNNNNNNNNN NNNNNNNNNN Ngtttttgta ctctcaGAAA tgcagaagct acaaagata aggcttcatgccgaaatcaacaccctgtcattttatggcagggtgtTTTTTT (SEQ ID NO: 7); (4) NNNNNNNNNN NNNNNNNNNNN gttttagagc taGAAAtagc aagttaaaat aaggctagtc cgttatcaac ttgaaaaagt ggcaccgagt cggtgcTTTT TT (SEQ ID NO: 8); (5) NNNNNNNNNN NNNNNNNNNN gttttagagc taGAAATAGc aagttaaaat aaggctagtccgttatcaacttgaaaaagtgTTTTTTT (SEQ ID NO: 9); and (6) NNNNNNNNNN NNNNNNNNNN gttttagagc tagAAATAGc aagttaaaat aaggctagtc cgttatca TTTTTTTT (SEQ ID NO: 10). In some embodiments, sequences (1) to (3) are used in combination with Cas9 from S. thermophilus CRISPR1. In some embodiments, sequences (4) to (6) are used in combination with Cas9 from S. pyogenes. In some embodiments, the tracr sequence is a separate transcript from a transcript comprising the tracr mate sequence (such as illustrated in the top portion of FIG. 11B).

In some embodiments, the CRISPR enzyme is part of a fusion protein comprising one or more heterologous protein domains (e.g. about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more domains in addition to the CRISPR enzyme). A CRISPR enzyme fusion protein may comprise any additional protein sequence, and optionally a linker sequence between any two domains. Examples of protein domains that may be fused to a CRISPR enzyme include, without limitation, epitope tags, reporter gene sequences, and protein domains having one or more of the following activities: methylase activity, demethylase activity, transcription activation activity, transcription repression activity, transcription release factor activity, histone modification activity, RNA cleavage activity and nucleic acid binding activity. Non-limiting examples of epitope tags include histidine (His) tags, V5 tags, FLAG tags, influenza hemagglutinin (HA) tags, Myc tags, VSV-G tags, and thioredoxin (Trx) tags. Examples of reporter genes include, but are not limited to, glutathione-S-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransferase (CAT) beta-galactosidase, beta-glucuronidase, luciferase, green fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and autofluorescent proteins including blue fluorescent protein (BFP). A CRISPR enzyme may be fused to a gene sequence encoding a protein or a fragment of a protein that bind DNA molecules or bind other cellular molecules, including but not limited to maltose binding protein (MBP), S-tag, Lex A DNA binding domain (DBD) fusions, GAL4 DNA binding domain fusions, and herpes simplex virus (HSV) BP16 protein fusions. Additional domains that may form part of a fusion protein comprising a CRISPR enzyme are described in US20110059502, incorporated herein by reference. In some embodiments, a tagged CRISPR enzyme is used to identify the location of a target sequence.

In an aspect of the invention, a reporter gene which includes but is not limited to glutathione-S-transferase (GST), horseradish peroxidase (HRP), chloramphenicol acetyltransferase (CAT) beta-galactosidase, beta-glucuronidase, luciferase, green fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and autofluorescent proteins including blue fluorescent protein (BFP), may be introduced into a cell to encode a gene product which serves as a marker by which to measure the alteration or modification of expression of the gene product. In a further embodiment of the invention, the DNA molecule encoding the gene product may be introduced into the cell via a vector. In a preferred embodiment of the invention the gene product is luciferase. In a further embodiment of the invention the expression of the gene product is decreased.

In some aspects, the invention provides methods comprising delivering one or more polynucleotides, such as or one or more vectors as described herein, one or more transcripts thereof, and/or one or proteins transcribed therefrom, to a host or target cell. In some aspects, the invention further provides cells produced by such methods, and organisms (such as animals, plants, or fungi) comprising or produced from such cells. In some embodiments, a CRISPR enzyme in combination with (and optionally complexed with) a guide sequence is delivered to a cell. Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids in mammalian cells or target tissues. Such methods can be used to administer nucleic acids encoding components of a CRISPR system to cells in culture, or in a host organism. Non-viral vector delivery systems include DNA plasmids, RNA (e.g. a transcript of a vector described herein), naked nucleic acid, and nucleic acid complexed with a delivery vehicle, such as a liposome. Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell. For a review of gene therapy procedures, see Anderson, Science 256:808-813 (1992); Nabel & Felgner, TIBTECH 11:211-217 (1993); Mitani & Caskey, TIBTECH 11:162-166 (1993); Dillon, TIBTECH 11:167-175 (1993); Miller, Nature 357:455-460 (1992); Van Brunt, Biotechnology 6(10):1149-1154 (1988); Vigne, Restorative Neurology and Neuroscience 8:35-36 (1995); Kremer & Perricaudet, British Medical Bulletin 51(1):31-44 (1995); Haddada et al., in Current Topics in Microbiology and Immunology Doerfler and Bohm (eds) (1995); and Yu et al., Gene Therapy 1:13-26 (1994). Methods of non-viral delivery of nucleic acids include lipofection, nucleofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipid:nucleic acid conjugates, naked DNA, artificial virions, and agent-enhanced uptake of DNA. Lipofection is described in e.g., U.S. Pat. Nos. 5,049,386, 4,946,787; and 4,897,355) and lipofection reagents are sold commercially (e.g., Transfectam™ and Lipofectin™). Cationic and neutral lipids that are suitable for efficient receptor-recognition lipofection of polynucleotides include those of Felgner, WO 91/17424; WO 91/16024. Delivery can be to cells (e.g. in vitro or ex vivo administration) or target tissues (e.g. in vivo administration).

The preparation of lipid:nucleic acid complexes, including targeted liposomes such as immunolipid complexes, is well known to one of skill in the art (see, e.g., Crystal, Science 270:404-410 (1995); Blaese et al., Cancer Gene Ther. 2:291-297 (1995); Behr et al., Bioconjugate Chem. 5:382-389 (1994); Remy et al., Bioconjugate Chem. 5:647-654 (1994); Gao et al., Gene Therapy 2:710-722 (1995); Ahmad et al., Cancer Res. 52:4817-4820 (1992); U.S. Pat. Nos. 4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728, 4,774,085, 4,837,028, and 4,946,787).

The use of RNA or DNA viral based systems for the delivery of nucleic acids take advantage of highly evolved processes for targeting a virus to specific cells in the body and trafficking the viral payload to the nucleus. Viral vectors can be administered directly to patients (in vivo) or they can be used to treat cells in vitro, and the modified cells may optionally be administered to patients (ex vivo). Conventional viral based systems could include retroviral, lentivirus, adenoviral, adeno-associated and herpes simplex virus vectors for gene transfer. Integration in the host genome is possible with the retrovirus, lentivirus, and adeno-associated virus gene transfer methods, often resulting in long term expression of the inserted transgene. Additionally, high transduction efficiencies have been observed in many different cell types and target tissues.

The tropism of a retrovirus can be altered by incorporating foreign envelope proteins, expanding the potential target population of target cells. Lentiviral vectors are retroviral vectors that are able to transduce or infect non-dividing cells and typically produce high viral titers. Selection of a retroviral gene transfer system would therefore depend on the target tissue. Retroviral vectors are comprised of cis-acting long terminal repeats with packaging capacity for up to 6-10 kb of foreign sequence. The minimum cis-acting LTRs are sufficient for replication and packaging of the vectors, which are then used to integrate the therapeutic gene into the target cell to provide permanent transgene expression. Widely used retroviral vectors include those based upon murine leukemia virus (MuLV), gibbon ape leukemia virus (GaLV), Simian Immuno deficiency virus (SIV), human immuno deficiency virus (HIV), and combinations thereof (see, e.g., Buchscher et al., J. Virol. 66:2731-2739 (1992); Johann et al., J. Virol. 66:1635-1640 (1992); Sommnerfelt et al., Virol. 176:58-59 (1990); Wilson et al., J. Virol. 63:2374-2378 (1989); Miller et al., J. Virol. 65:2220-2224 (1991); PCT/US94/05700),In applications where transient expression is preferred, adenoviral based systems may be used. Adenoviral based vectors are capable of very high transduction efficiency in many cell types and do not require cell division. With such vectors, high titer and levels of expression have been obtained. This vector can be produced in large quantities in a relatively simple system. Adeno-associated virus (“AAV”) vectors may also be used to transduce cells with target nucleic acids, e.g., in the in vitro production of nucleic acids and peptides, and for in vivo and ex vivo gene therapy procedures (see, e.g., West et al., Virology 160:38-47 (1987); U.S. Pat. No. 4,797,368; WO 93/24641; Kotin, Human Gene Therapy 5:793-801 (1994); Muzyczka, J. Clin. Invest. 94:1351 (1994). Construction of recombinant AAV vectors are described in a number of publications, including U.S. Pat. No. 5,173,414; Tratschin et al., Mol. Cell. Biol. 5:3251-3260 (1985); Tratschin, et al., Mol. Cell. Biol. 4:2072-2081 (1984); Hermonat & Muzyczka, PNAS 81:6466-6470 (1984); and Samulski et al., J. Virol. 63:03822-3828 (1989).

Packaging cells are typically used to form virus particles that are capable of infecting a host cell. Such cells include 293 cells, which package adenovirus, and w2 cells or PA317 cells, which package retrovirus. Viral vectors used in gene therapy are usually generated by producing a cell line that packages a nucleic acid vector into a viral particle. The vectors typically contain the minimal viral sequences required for packaging and subsequent integration into a host, other viral sequences being replaced by an expression cassette for the polynucleotide(s) to be expressed. The missing viral functions are typically supplied in trans by the packaging cell line. For example, AAV vectors used in gene therapy typically only possess ITR sequences from the AAV genome which are required for packaging and integration into the host genome. Viral DNA is packaged in a cell line, which contains a helper plasmid encoding the other AAV genes, namely rep and cap, but lacking ITR sequences. The cell line may also be infected with adenovirus as a helper. The helper virus promotes replication of the AAV vector and expression of AAV genes from the helper plasmid. The helper plasmid is not packaged in significant amounts due to a lack of ITR sequences. Contamination with adenovirus can be reduced by, e.g., heat treatment to which adenovirus is more sensitive than AAV. Additional methods for the delivery of nucleic acids to cells are known to those skilled in the art. See, for example, US20030087817, incorporated herein by reference.

In some embodiments, a host cell is transiently or non-transiently transfected with one or more vectors described herein to arrive at a tissue culture model. In some embodiments, a cell is transfected as it naturally occurs in a subject. In some embodiments, a cell that is transfected is taken from a subject. In some embodiments, the cell is derived from cells taken from a subject, such as a cell line. A wide variety of cell lines for tissue culture models are known in the art. Examples of cell lines include, but are not limited to, C8161, CCRF-CEM, MOLT, mIMCD-3, NHDF, HeLa-S3, Huhl, Huh4, Huh7, HUVEC, HASMC, HEKn, HEKa, MiaPaCell, Pancl, PC-3, TF1, CTLL-2, C1R, Rath, CV1, RPTE, A10, T24, J82, A375, ARH-77, Calul, SW480, SW620, SKOV3, SK-UT, CaCo2, P388D1, SEM-K2, WEHI-231, HB56, Jurkat, J45.01, LRMB, Bc1-1, BC-3, IC21, DLD2, Raw264.7, NRK, NRK-52E, MRCS, MEF, Hep G2, HeLa B, HeLa T4, COS, COS-1, COS-6, COS-M6A, BS-C-1 monkey kidney epithelial, BALB/3T3 mouse embryo fibroblast, 3T3 Swiss, 3T3-L1, 132-d5 human fetal fibroblasts; 10.1 mouse fibroblasts, 293-T, 3T3, 721, 9L, A2780, A2780ADR, A2780cis, A172, A20, A253, A431, A-549, ALC, B16, B35, BCP-1 cells, BEAS-2B, bEnd.3, BHK-21, BR 293, BxPC3, C3H-10T1/2, C6/36, Cal-27, CHO, CHO-7, CHO-IR, CHO-K1, CHO-K2, CHO-T, CHO Dhfr −/−, COR-L23, COR-L23/CPR, COR-L23/5010, COR-L23/R23, COS-7, COV-434, CML T1, CMT, CT26, D17, DH82, DU145, DuCaP, EL4, EM2, EM3, EMT6/AR1, EMT6/AR10.0, FM3, H1299, H69, HB54, HB55, HCA2, HEK-293, HeLa, Hepa1c1c7, HL-60, HMEC, HT-29, Jurkat, JY cells, K562 cells, Ku812, KCL22, KG1, KYO1, LNCap, Ma-Mel 1-48, MC-38, MCF-7, MCF-10A, MDA-MB-231, MDA-MB-468, MDA-MB-435, MDCK II, MDCK II, MOR/0.2R, MONO-MAC 6, MTD-1A, MyEnd, NCI-H69/CPR, NCI-H69/LX10, NCI-H69/LX20, NCI-H69/LX4, NIH-3T3, NALM-1, NW-145, OPCN/OPCT cell lines, Peer, PNT-1A/PNT 2, RenCa, RIN-5F, RMA/RMAS, Saos-2 cells, Sf-9, SkBr3, T2, T-47D, T84, THP1 cell line, U373, U87, U937, VCaP, Vero cells, WM39, WT-49, X63, YAC-1, YAR, and transgenic varieties thereof. In a preferred embodiment of the invention the cells that relate to aspects of the invention are HEK293FT cells. Cell lines are available from a variety of sources known to those with skill in the art (see, e.g., the American Type Culture Collection (ATCC) (Manassas, Va.)). In some embodiments, a cell transfected with one or more vectors described herein is used to establish a new cell line comprising one or more vector-derived sequences. In some embodiments, a cell transiently transfected with the components of a CRISPR system as described herein (such as by transient transfection of one or more vectors, or transfection with RNA), and modified through the activity of a CRISPR complex, is used to establish a new cell line comprising cells containing the modification but lacking any other exogenous sequence. In some embodiments, cells transiently or non-transiently transfected with one or more vectors described herein, or cell lines derived from such cells are used in assessing one or more test compounds.

In some embodiments, one or more vectors described herein are used to transfect cells from a non-human transgenic animal or transgenic plant. In some embodiments, the transgenic animal is a mammal, such as a mouse, rat, or rabbit. In certain embodiments, the organism or subject is a plant. In certain embodiments, the organism or subject or plant is algae. Cells from transgenic animals are also provided, as are transgenic plants, especially crops and algae. The cells of a transgenic animal or plant may be useful in applications outside of providing a disease model. In this regard, cells from transgenic plants, especially pulses and tubers, and animals, especially mammals such as livestock (cows, sheep, goats and pigs), but also poultry and edible insects, are preferred.

In one aspect, the invention provides for methods of modifying a target polynucleotide in a eukaryotic cell, which may be in vivo, ex vivo or in vitro. In some embodiments, the method comprises sampling a cell or population of cells from a human or non-human animal or plant (including micro-algae), and modifying the cell or cells. Culturing may occur at any stage ex vivo. The cell or cells may even be re-introduced into the non-human animal or plant (including micro-algae).

In one aspect, the invention provides for methods of modifying a target polynucleotide in a eukaryotic cell. In some embodiments, the method comprises allowing a CRISPR complex to bind to the target polynucleotide to effect cleavage of said target polynucleotide thereby modifying the target polynucleotide, wherein the CRISPR complex comprises a CRISPR enzyme complexed with a guide sequence hybridized to a target sequence within said target polynucleotide, wherein said guide sequence is linked to a tracr mate sequence which in turn hybridizes to a tracr sequence.

In one aspect, the invention provides a method of modifying expression of a polynucleotide in a eukaryotic cell. In some embodiments, the method comprises allowing a CRISPR complex to bind to the polynucleotide such that said binding results in increased or decreased expression of said polynucleotide; wherein the CRISPR complex comprises a CRISPR enzyme complexed with a guide sequence hybridized to a target sequence within said polynucleotide, wherein said guide sequence is linked to a tracr mate sequence which in turn hybridizes to a tracr sequence.

With recent advances in crop genomics, the ability to use CRISPR-Cas systems to perform efficient and cost effective gene editing and manipulation will allow the rapid selection and comparison of single and multiplexed genetic manipulations to transform such genomes for improved production and enhanced traits. In this regard reference is made to US patents and publications: U.S. Pat. No. 6,603,061—Agrobacterium-Mediated Plant Transformation Method; U.S. Pat. No. 7,868,149—Plant Genome Sequences and Uses Thereof and US 2009/0100536—Transgenic Plants with Enhanced Agronomic Traits, all the contents and disclosure of each of which are herein incorporated by reference in their entirety. In the practice of the invention, the contents and disclosure of Morrell et al “Crop genomics:advances and applications” Nat Rev Genet. 2011 Dec. 29; 13(2):85-96 are also herein incorporated by reference in their entirety. In some methods of the invention the vector is an Agrobacterium Ti or Ri plasmid for use in plants.

In plants, pathogens are often host-specific. For example, Fusarium oxysporum f. sp. lycopersici causes tomato wilt but attacks only tomato, and F. oxysporum f. dianthii Puccinia graminis f. sp. tritici attacks only wheat. Plants have existing and induced defenses to resist most pathogens. Mutations and recombination events across plant generations lead to genetic variability that gives rise to susceptibility or reduced susceptibility or resistance, especially as pathogens reproduce with more frequency than plants. In plants there can be non-host resistance, e.g., the host and pathogen are incompatible. There can also be Horizontal Resistance, e.g., partial resistance against all races of a pathogen, typically controlled by many genes and Vertical Resistance, e.g., complete resistance to some races of a pathogen but not to other races, typically controlled by a few genes. In a Gene-for-Gene level, plants and pathogens evolve together, and the genetic changes in one balance changes in other. Accordingly, using Natural Variability, breeders combine most useful genes for Yield, Quality, Uniformity, Hardiness, Resistance. The sources of resistance genes include native or foreign Varieties, Heirloom Varieties, Wild Plant Relatives, and Induced Mutations, e.g., treating plant material with mutagenic agents. Using the present invention, plant breeders are provided with a new tool to induce mutations. Accordingly, one skilled in the art can analyze the genome of sources of resistance genes, and in Varieties having desired characteristics or traits employ the present invention to induce the rise of resistance genes, with more precision than previous mutagenic agents and hence accelerate and improve plant breeding programs.

Screening can involve guide library synthesis, cloning of the guide RNA into a vector library to deliver the guides to cells, and the vector can include nucleic acid molecules to express Cas9 or the vector can be sequenctially or co-delivered with one or more other vectors to deliver CRISPR-Cas9 system components, e.g., a second vector that contains nucleic acid molecules to express Cas9, or the cells can be otherwise engineered to express Cas9, whereby the CRISPR-cas system forms. The vector can be any suitable vector for delivery to the desired cell. Many such vectors are herein disclosed, including as to all cells mentioned herein; for instance, as to plants various vectors useful in the practice of the invention are also discussed in the context of crop genomics. The formed CRISPR-Cas9 system can give rise to mutations, e.g., breaks, or nicks, deletions, insertions, or substitutions. As members of the library may target different positions within the DNA of the cells, a library of cells, with potentially multiple genotypes arises. Such mutations may give rise to a desired phenotype. Thus, the library or libraries of cells are screened for selection of the desired phenotype. As to plants, CRISPR-Cas9 allows for targeted mutagenesis, e.g., CRISPR-Cas9 can be a mutagenic agent, plants expressing a desired phenotype from the mutation, e.g., reduced susceptibility or resistance to a pathogen or plant disease, are therefore better identified because the CRISPR-Cas9 system and the nature of the mutation can be correlated, e.g., based on the CRISPR-Cas9, e.g., guide sequence thereof, that induced a favorable mutation, one can appreciate where there was binding, and based on other aspects of the particular CRISPR-Cas9 system, the favorable mutation arising from CRISPR-Cas9 as a mutagenic agent can provide where and how the Cas9 of the system acted; and hence where and how, e.g., the nature of the mutation, is divined by screening using CRISPR-Cas9. Likewise, one can target particular portions of a cell, e.g., plant cell, genome by selection of a CRISPR-Cas9 library directed to portions of that genome, whereby a population having targeted mutations arises, and from the phenotypes of the cells, the skilled person can readily correlate the mutations made to the phenotypes observed, such that when a favorable phenotype is observed, the nature of the CRISPR-Cas9 can provide information as to binding and the nature of the mutation that gave rise to the favorable phenotype, and this can be useful to ascertain whether certain mutations can indeed give rise to favorable phenotypes. CRISPR-Cas9 can be used for revealing and engineering gene functions, including as to all cells mentioned herein, including, for instance plants (including microalgae). Accordingly, CRISPR-Cas9 libraries are a tool, including in creating or screening plant populations, e.g., plant or crop genetics, breeding. Moreover, as there are the GeCKO libraries corresponding to the mouse and human genomes, from this disclosure all that it presents to the knowledge in the art, Applicants believe one skilled in the art can create libraries analogous to the mouse and human GeCKO libraries for any plant without any undue experimentation.

In one aspect, the invention provides kits containing any one or more of the elements disclosed in the above methods and compositions. In some embodiments, the kit comprises a vector system and instructions for using the kit. In some embodiments, the vector system comprises (a) a first regulatory element operably linked to a tracr mate sequence and one or more insertion sites for inserting a guide sequence upstream of the tracr mate sequence, wherein when expressed, the guide sequence directs sequence-specific binding of a CRISPR complex to a target sequence in a eukaryotic cell, wherein the CRISPR complex comprises a CRISPR enzyme complexed with (1) the guide sequence that is hybridizable to the target sequence, and (2) the tracr mate sequence that is hybridized to the tracr sequence; and/or (b) a second regulatory element operably linked to an enzyme-coding sequence encoding said CRISPR enzyme comprising a nuclear localization sequence. Elements may be provided individually or in combinations, and may be provided in any suitable container, such as a vial, a bottle, or a tube. In some embodiments, the kit includes instructions in one or more languages, for example in more than one language.

In some embodiments, a kit comprises one or more reagents for use in a process utilizing one or more of the elements described herein. Reagents may be provided in any suitable container. For example, a kit may provide one or more reaction or storage buffers. Reagents may be provided in a form that is usable in a particular assay, or in a form that requires addition of one or more other components before use (e.g. in concentrate or lyophilized form). A buffer can be any buffer, including but not limited to a sodium carbonate buffer, a sodium bicarbonate buffer, a borate buffer, a Tris buffer, a MOPS buffer, a HEPES buffer, and combinations thereof. In some embodiments, the buffer is alkaline. In some embodiments, the buffer has a pH from about 7 to about 10. In some embodiments, the kit comprises one or more oligonucleotides corresponding to a guide sequence for insertion into a vector so as to operably link the guide sequence and a regulatory element. In some embodiments, the kit comprises a homologous recombination template polynucleotide.

In one aspect, the invention provides methods for using one or more elements of a CRISPR system. The CRISPR complex of the invention provides an effective means for modifying a target polynucleotide. The CRISPR complex of the invention has a wide variety of utility including modifying (e.g., deleting, inserting, translocating, inactivating, activating) a target polynucleotide in a multiplicity of cell types. As such the CRISPR complex of the invention has a broad spectrum of applications in, e.g., gene therapy, drug screening, disease diagnosis, and prognosis. An exemplary CRISPR complex comprises a CRISPR enzyme complexed with a guide sequence hybridized to a target sequence within the target polynucleotide. The guide sequence is linked to a tracr mate sequence, which in turn hybridizes to a tracr sequence.

The target polynucleotide of a CRISPR complex can be any polynucleotide endogenous or exogenous to the eukaryotic cell. For example, the target polynucleotide can be a polynucleotide residing in the nucleus of the eukaryotic cell. The target polynucleotide can be a sequence coding a gene product (e.g., a protein) or a non-coding sequence (e.g., a regulatory polynucleotide or a junk DNA). Without wishing to be bound by theory, it is believed that the target sequence should be associated with a PAM (protospacer adjacent motif); that is, a short sequence recognized by the CRISPR complex. The precise sequence and length requirements for the PAM differ depending on the CRISPR enzyme used, but PAMs are typically 2-5 base pair sequences adjacent the protospacer (that is, the target sequence). Examples of PAM sequences are given in the examples below, and the skilled person will be able to identify further PAM sequences for use with a given CRISPR enzyme.

The target polynucleotide of a CRISPR complex may include a number of disease-associated genes and polynucleotides as well as signaling biochemical pathway-associated genes and polynucleotides as listed in U.S. provisional patent applications 61/736,527 and 61/748,427 having Broad reference BI-2011/008/WSGR Docket No. 44063-701.101 and BI-2011/008/WSGR Docket No. 44063-701.102 respectively, both entitled SYSTEMS METHODS AND COMPOSITIONS FOR SEQUENCE MANIPULATION filed on Dec. 12, 2012 and Jan. 2, 2013, respectively, the contents of all of which are herein incorporated by reference in their entirety. The target polynucleotide of a CRISPR complex can be a gene of previously unknown function wherein its presence or absence in a screen (integrated barcode of the sgRNA) reveals details about its function. The target polynucleotide of a CRISPR complex may also be a gene whose interaction with the screening agent (eg. drug or other selection agent) is discovered through its presence or absence in cells (barcode of the sgRNA) in the screen. Hence, in an aspect of the invention new drugs or pharmaceutical compositions may be tested for performance against all possible genetic KOs (or a subset of possible KOs; for example, genes associated with a particular enzymatic pathway) to understand how different organisms, e.g., humans (who carry different genetic KOs) might react to the drug and in which genetic background the drug might work better or worse.

Examples of genes and genomic loci that may be targeted by the CRISPR-Cas system guide RNA sequences described in Tables 1 and 10 (as provided in the compact discs created Apr. 11, 2014, as filed in connection with U.S. applications 61/960,777 and 61/995,636) may include but are not limited to sequences associated with a signaling biochemical pathway, e.g., a signaling biochemical pathway-associated gene or polynucleotide. Examples of target polynucleotides include a disease associated gene or polynucleotide. A “disease-associated” gene or polynucleotide refers to any gene or polynucleotide which is yielding transcription or translation products at an abnormal level or in an abnormal form in cells derived from a disease-affected tissues compared with tissues or cells of a non disease control. It may be a gene that becomes expressed at an abnormally high level; it may be a gene that becomes expressed at an abnormally low level, where the altered expression correlates with the occurrence and/or progression of the disease. A disease-associated gene also refers to a gene possessing mutation(s) or genetic variation that is directly responsible or is in linkage disequilibrium with a gene(s) that is responsible for the etiology of a disease. The transcribed or translated products may be known or unknown, and may be at a normal or abnormal level.

Examples of disease-associated genes and polynucleotides are available from McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, Md.) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, Md.), available on the World Wide Web.

Examples of disease-associated genes and polynucleotides are listed in Tables A and B. Disease specific information is available from McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, Md.) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, Md.), available on the World Wide Web. Examples of signaling biochemical pathway-associated genes and polynucleotides are listed in Table C.

Mutations in these genes and pathways can result in production of improper proteins or proteins in improper amounts which affect function. Further examples of genes, diseases and proteins are hereby incorporated by reference from U.S. Provisional applications 61/736,527 and 61/748,427. Such genes, proteins and pathways may be the target polynucleotide of a CRISPR complex.

TABLE A DISEASE/DISORDERS GENE(S) Neoplasia PTEN; ATM; ATR; EGFR; ERBB2; ERBB3; ERBB4; Notch1; Notch2; Notch3; Notch4; AKT; AKT2; AKT3; HIF; HIF1a; HIF3a; Met; HRG; Bcl2; PPAR alpha; PPAR gamma; WT1 (Wilms Tumor); FGF Receptor Family members (5 members: 1, 2, 3, 4, 5); CDKN2a; APC; RB (retinoblastoma); MEN1; VHL; BRCA1; BRCA2; AR (Androgen Receptor); TSG101; IGF; IGF Receptor; Igf1 (4 variants); Igf2 (3 variants); Igf 1 Receptor; Igf 2 Receptor; Bax; Bcl2; caspases family (9 members: 1, 2, 3, 4, 6, 7, 8, 9, 12); Kras; Apc Age-related Macular Aber; Ccl2; Cc2; cp (ceruloplasmin); Timp3; cathepsinD; Degeneration Vldlr; Ccr2 Schizophrenia Neuregulin1 (Nrg1); Erb4 (receptor for Neuregulin); Complexin1 (Cplx1); Tph1 Tryptophan hydroxylase; Tph2 Tryptophan hydroxylase 2; Neurexin 1; GSK3; GSK3a; GSK3b Disorders 5-HTT (Slc6a4); COMT; DRD (Drd1a); SLC6A3; DAOA; DTNBP1; Dao (Dao1) Trinucleotide Repeat HTT (Huntington's Dx); SBMA/SMAX1/AR (Kennedy's Disorders Dx); FXN/25 (Friedrich's Ataxia); ATX3 (Machado- Joseph's Dx); ATXN1 and ATXN2 (spinocerebellar ataxias); DMPK (myotonic dystrophy); Atrophin-1 and Atn1 (DRPLA Dx); CBP (Creb-BP-global instability); VLDLR (Alzheimer's); Atxn7; Atxn10 Fragile X Syndrome FMR2; FXR1; FXR2; mGLUR5 Secretase Related APH-1 (alpha and beta); Presenilin (Psen1); nicastrin Disorders (Ncstn); PEN-2 Others Nos1; Parp1; Nat1; Nat2 Prion-related disorders Prp ALS SOD1; ALS2; STEX; FUS; TARDBP; VEGF (VEGF-a; VEGF-b; VEGF-c) Drug addiction Prkce (alcohol); Drd2; Drd4; ABAT (alcohol); GRIA2; Grm5; Grin1; Htr1b; Grin2a; Drd3; Pdyn; Gria1 (alcohol) Autism Mecp2; BZRAP1; MDGA2; Sema5A; Neurexin 1; Fragile X (FMR2 (AFF2); FXR1; FXR2; Mglur5) Alzheimer's Disease E1; CHIP; UCH; UBB; Tau; LRP; PICALM; Clusterin; PS1; SORL1; CR1; Vldlr; Uba1; Uba3; CHIP28 (Aqp1, Aquaporin 1); Uchl1; Uchl3; APP Inflammation IL-10; IL-1 (IL-1a; IL-1b); IL-13; IL-17 (IL-17a (CTLA8); IL- 17b; IL-17c; IL-17d; IL-17f); II-23; Cx3cr1; ptpn22; TNFa; NOD2/CARD15 for IBD; IL-6; IL-12 (IL-12a; IL-12b); CTLA4; Cx3cl1 Parkinson's Disease x-Synuclein; DJ-1; LRRK2; Parkin; PINK1

TABLE B Blood and Anemia (CDAN1, CDA1, RPS19, DBA, PKLR, PK1, NT5C3, UMPH1, coagulation diseases PSN1, RHAG, RH50A, NRAMP2, SPTB, ALAS2, ANH1, ASB, and disorders ABCB7, ABC7, ASAT); Bare lymphocyte syndrome (TAPBP, TPSN, TAP2, ABCB3, PSF2, RING11, MHC2TA, C2TA, RFX5, RFXAP, RFX5), Bleeding disorders (TBXA2R, P2RX1, P2X1); Factor H and factor H-like 1 (HF1, CFH, HUS); Factor V and factor VIII (MCFD2); Factor VII deficiency (F7); Factor X deficiency (F10); Factor XI deficiency (F11); Factor XII deficiency (F12, HAF); Factor XIIIA deficiency (F13A1, F13A); Factor XIIIB deficiency (F13B); Fanconi anemia (FANCA, FACA, FA1, FA, FAA, FAAP95, FAAP90, FLJ34064, FANCB, FANCC, FACC, BRCA2, FANCD1, FANCD2, FANCD, FACD, FAD, FANCE, FACE, FANCF, XRCC9, FANCG, BRIP1, BACH1, FANCJ, PHF9, FANCL, FANCM, KIAA1596); Hemophagocytic lymphohistiocytosis disorders (PRF1, HPLH2, UNC13D, MUNC13-4, HPLH3, HLH3, FHL3); Hemophilia A (F8, F8C, HEMA); Hemophilia B (F9, HEMB), Hemorrhagic disorders (PI, ATT, F5); Leukocyde deficiencies and disorders (ITGB2, CD18, LCAMB, LAD, EIF2B1, EIF2BA, EIF2B2, EIF2B3, EIF2B5, LVWM, CACH, CLE, EIF2B4); Sickle cell anemia (HBB); Thalassemia (HBA2, HBB, HBD, LCRB, HBA1). Cell dysregulation B-cell non-Hodgkin lymphoma (BCL7A, BCL7); Leukemia (TAL1, and oncology TCL5, SCL, TAL2, FLT3, NBS1, NBS, ZNFN1A1, IK1, LYF1, diseases and disorders HOXD4, HOX4B, BCR, CML, PHL, ALL, ARNT, KRAS2, RASK2, GMPS, AF10, ARHGEF12, LARG, KIAA0382, CALM, CLTH, CEBPA, CEBP, CHIC2, BTL, FLT3, KIT, PBT, LPP, NPM1, NUP214, D9S46E, CAN, CAIN, RUNX1, CBFA2, AML1, WHSC1L1, NSD3, FLT3, AF1Q, NPM1, NUMA1, ZNF145, PLZF, PML, MYL, STAT5B, AF10, CALM, CLTH, ARL11, ARLTS1, P2RX7, P2X7, BCR, CML, PHL, ALL, GRAF, NF1, VRNF, WSS, NFNS, PTPN11, PTP2C, SHP2, NS1, BCL2, CCND1, PRAD1, BCL1, TCRA, GATA1, GF1, ERYF1, NFE1, ABL1, NQO1, DIA4, NMOR1, NUP214, D9S46E, CAN, CAIN). Inflammation and AIDS (KIR3DL1, NKAT3, NKB1, AMB11, KIR3DS1, IFNG, CXCL12, immune related SDF1); Autoimmune lymphoproliferative syndrome (TNFRSF6, APT1, diseases and disorders FAS, CD95, ALPS1A); Combined immunodeficiency, (IL2RG, SCIDX1, SCIDX, IMD4); HIV-1 (CCL5, SCYA5, D17S136E, TCP228), HIV susceptibility or infection (IL10, CSIF, CMKBR2, CCR2, CMKBR5, CCCKR5 (CCR5)); Immunodeficiencies (CD3E, CD3G, AICDA, AID, HIGM2, TNFRSF5, CD40, UNG, DGU, HIGM4, TNFSF5, CD40LG, HIGM1, IGM, FOXP3, IPEX, AIID, XPID, PIDX, TNFRSF14B, TACI); Inflammation (IL-10, IL-1 (IL-1a, IL-1b), IL-13, IL-17 (IL-17a (CTLA8), IL-17b, IL-17c, IL-17d, IL-17f), II-23, Cx3cr1, ptpn22, TNFa, NOD2/CARD15 for IBD, IL-6, IL-12 (IL-12a, IL-12b), CTLA4, Cx3cl1); Severe combined immunodeficiencies (SCIDs)(JAK3, JAKL, DCLRE1C, ARTEMIS, SCIDA, RAG1, RAG2, ADA, PTPRC, CD45, LCA, IL7R, CD3D, T3D, IL2RG, SCIDX1, SCIDX, IMD4). Metabolic, liver, Amyloid neuropathy (TTR, PALB); Amyloidosis (APOA1, APP, AAA, kidney and protein CVAP, AD1, GSN, FGA, LYZ, TTR, PALB); Cirrhosis (KRT18, KRT8, diseases and disorders CIRH1A, NAIC, TEX292, KIAA1988); Cystic fibrosis (CFTR, ABCC7, CF, MRP7); Glycogen storage diseases (SLC2A2, GLUT2, G6PC, G6PT, G6PT1, GAA, LAMP2, LAMPB, AGL, GDE, GBE1, GYS2, PYGL, PFKM); Hepatic adenoma, 142330 (TCF1, HNF1A, MODY3), Hepatic failure, early onset, and neurologic disorder (SCOD1, SCO1), Hepatic lipase deficiency (LIPC), Hepatoblastoma, cancer and carcinomas (CTNNB1, PDGFRL, PDGRL, PRLTS, AXIN1, AXIN, CTNNB1, TP53, P53, LFS1, IGF2R, MPRI, MET, CASP8, MCH5; Medullary cystic kidney disease (UMOD, HNFJ, FJHN, MCKD2, ADMCKD2); Phenylketonuria (PAH, PKU1, QDPR, DHPR, PTS); Polycystic kidney and hepatic disease (FCYT, PKHD1, ARPKD, PKD1, PKD2, PKD4, PKDTS, PRKCSH, G19P1, PCLD, SEC63). Muscular/Skeletal Becker muscular dystrophy (DMD, BMD, MYF6), Duchenne Muscular diseases and disorders Dystrophy (DMD, BMD); Emery-Dreifuss muscular dystrophy (LMNA, LMN1, EMD2, FPLD, CMD1A, HGPS, LGMD1B, LMNA, LMN1, EMD2, FPLD, CMD1A); Facioscapulohumeral muscular dystrophy (FSHMD1A, FSHD1A); Muscular dystrophy (FKRP, MDC1C, LGMD2I, LAMA2, LAMM, LARGE, KIAA0609, MDC1D, FCMD, TTID, MYOT, CAPN3, CANP3, DYSF, LGMD2B, SGCG, LGMD2C, DMDA1, SCG3, SGCA, ADL, DAG2, LGMD2D, DMDA2, SGCB, LGMD2E, SGCD, SGD, LGMD2F, CMD1L, TCAP, LGMD2G, CMD1N, TRIM32, HT2A, LGMD2H, FKRP, MDC1C, LGMD2I, TTN, CMD1G, TMD, LGMD2J, POMT1, CAV3, LGMD1C, SEPN1, SELN, RSMD1, PLEC1, PLTN, EBS1); Osteopetrosis (LRP5, BMND1, LRP7, LR3, OPPG, VBCH2, CLCN7, CLC7, OPTA2, OSTM1, GL, TCIRG1, TIRC7, OC116, OPTB1); Muscular atrophy (VAPB, VAPC, ALS8, SMN1, SMA1, SMA2, SMA3, SMA4, BSCL2, SPG17, GARS, SMAD1, CMT2D, HEXB, IGHMBP2, SMUBP2, CATF1, SMARD1). Neurological and ALS (SOD1, ALS2, STEX, FUS, TARDBP, VEGF (VEGF-a, VEGF-b, neuronal diseases and VEGF-c); Alzheimer disease (APP, AAA, CVAP, AD1, APOE, AD2, disorders PSEN2, AD4, STM2, APBB2, FE65L1, NOS3, PLAU, URK, ACE, DCP1, ACE1, MPO, PACIP1, PAXIP1L, PTIP, A2M, BLMH, BMH, PSEN1, AD3); Autism (Mecp2, BZRAP1, MDGA2, Sema5A, Neurexin 1, GLO1, MECP2, RTT, PPMX, MRX16, MRX79, NLGN3, NLGN4, KIAA1260, AUTSX2); Fragile X Syndrome (FMR2, FXR1, FXR2, mGLUR5); Huntington's disease and disease like disorders (HD, IT15, PRNP, PRIP, JPH3, JP3, HDL2, TBP, SCA17); Parkinson disease (NR4A2, NURR1, NOT, TINUR, SNCAIP, TBP, SCA17, SNCA, NACP, PARK1, PARK4, DJ1, PARK7, LRRK2, PARK8, PINK1, PARK6, UCHL1, PARK5, SNCA, NACP, PARK1, PARK4, PRKN, PARK2, PDJ, DBH, NDUFV2); Rett syndrome (MECP2, RTT, PPMX, MRX16, MRX79, CDKL5, STK9, MECP2, RTT, PPMX, MRX16, MRX79, x-Synuclein, DJ-1); Schizophrenia (Neuregulin1 (Nrg1), Erb4 (receptor for Neuregulin), Complexin1 (Cplx1), Tph1 Tryptophan hydroxylase, Tph2, Tryptophan hydroxylase 2, Neurexin 1, GSK3, GSK3a, GSK3b, 5-HTT (Slc6a4), COMT, DRD (Drd1a), SLC6A3, DAOA, DTNBP1, Dao (Dao1)); Secretase Related Disorders (APH-1 (alpha and beta), Presenilin (Psen1), nicastrin, (Ncstn), PEN-2, Nos1, Parp1, Nat1, Nat2); Trinucleotide Repeat Disorders (HTT (Huntington's Dx), SBMA/SMAX1/AR (Kennedy's Dx), FXN/X25 (Friedrich's Ataxia), ATX3 (Machado-Joseph's Dx), ATXN1 and ATXN2 (spinocerebellar ataxias), DMPK (myotonic dystrophy), Atrophin-1 and Atn1 (DRPLA Dx), CBP (Creb-BP-global instability), VLDLR (Alzheimer's), Atxn7, Atxn10). Occular diseases and Age-related macular degeneration (Abcr, Ccl2, Cc2, cp (ceruloplasmin), disorders Timp3, cathepsinD, Vldlr, Ccr2); Cataract (CRYAA, CRYA1, CRYBB2, CRYB2, PITX3, BFSP2, CP49, CP47, CRYAA, CRYA1, PAX6, AN2, MGDA, CRYBA1, CRYB1, CRYGC, CRYG3, CCL, LIM2, MP19, CRYGD, CRYG4, BFSP2, CP49, CP47, HSF4, CTM, HSF4, CTM, MIP, AQP0, CRYAB, CRYA2, CTPP2, CRYBB1, CRYGD, CRYG4, CRYBB2, CRYB2, CRYGC, CRYG3, CCL, CRYAA, CRYA1, GJA8, CX50, CAE1, GJA3, CX46, CZP3, CAE3, CCM1, CAM, KRIT1); Corneal clouding and dystrophy (APOA1, TGFBI, CSD2, CDGG1, CSD, BIGH3, CDG2, TACSTD2, TROP2, M1S1, VSX1, RINX, PPCD, PPD, KTCN, COL8A2, FECD, PPCD2, PIP5K3, CFD); Cornea plana congenital (KERA, CNA2); Glaucoma (MYOC, TIGR, GLC1A, JOAG, GPOA, OPTN, GLC1E, FIP2, HYPL, NRP, CYP1B1, GLC3A, OPA1, NTG, NPG, CYP1B1, GLC3A); Leber congenital amaurosis (CRB1, RP12, CRX, CORD2, CRD, RPGRIP1, LCA6, CORD9, RPE65, RP20, AIPL1, LCA4, GUCY2D, GUC2D, LCA1, CORD6, RDH12, LCA3); Macular dystrophy (ELOVL4, ADMD, STGD2, STGD3, RDS, RP7, PRPH2, PRPH, AVMD, AOFMD, VMD2).

TABLE C CELLULAR FUNCTION GENES PI3K/AKT Signaling PRKCE; ITGAM; ITGA5; IRAK1; PRKAA2; EIF2AK2; PTEN; EIF4E; PRKCZ; GRK6; MAPK1; TSC1; PLK1; AKT2; IKBKB; PIK3CA; CDK8; CDKN1B; NFKB2; BCL2; PIK3CB; PPP2R1A; MAPK8; BCL2L1; MAPK3; TSC2; ITGA1; KRAS; EIF4EBP1; RELA; PRKCD; NOS3; PRKAA1; MAPK9; CDK2; PPP2CA; PIM1; ITGB7; YWHAZ; ILK; TP53; RAF1; IKBKG; RELB; DYRK1A; CDKN1A; ITGB1; MAP2K2; JAK1; AKT1; JAK2; PIK3R1; CHUK; PDPK1; PPP2R5C; CTNNB1; MAP2K1; NFKB1; PAK3; ITGB3; CCND1; GSK3A; FRAP1; SFN; ITGA2; TTK; CSNK1A1; BRAF; GSK3B; AKT3; FOXO1; SGK; HSP90AA1; RPS6KB1 ERK/MAPK Signaling PRKCE; ITGAM; ITGA5; HSPB1; IRAK1; PRKAA2; EIF2AK2; RAC1; RAP1A; TLN1; EIF4E; ELK1; GRK6; MAPK1; RAC2; PLK1; AKT2; PIK3CA; CDK8; CREB1; PRKCI; PTK2; FOS; RPS6KA4; PIK3CB; PPP2R1A; PIK3C3; MAPK8; MAPK3; ITGA1; ETS1; KRAS; MYCN; EIF4EBP1; PPARG; PRKCD; PRKAA1; MAPK9; SRC; CDK2; PPP2CA; PIM1; PIK3C2A; ITGB7; YWHAZ; PPP1CC; KSR1; PXN; RAF1; FYN; DYRK1A; ITGB1; MAP2K2; PAK4; PIK3R1; STAT3; PPP2R5C; MAP2K1; PAK3; ITGB3; ESR1; ITGA2; MYC; TTK; CSNK1A1; CRKL; BRAF; ATF4; PRKCA; SRF; STAT1; SGK Glucocorticoid Receptor RAC1; TAF4B; EP300; SMAD2; TRAF6; PCAF; ELK1; Signaling MAPK1; SMAD3; AKT2; IKBKB; NCOR2; UBE2I; PIK3CA; CREB1; FOS; HSPA5; NFKB2; BCL2; MAP3K14; STAT5B; PIK3CB; PIK3C3; MAPK8; BCL2L1; MAPK3; TSC22D3; MAPK10; NRIP1; KRAS; MAPK13; RELA; STAT5A; MAPK9; NOS2A; PBX1; NR3C1; PIK3C2A; CDKN1C; TRAF2; SERPINE1; NCOA3; MAPK14; TNF; RAF1; IKBKG; MAP3K7; CREBBP; CDKN1A; MAP2K2; JAK1; IL8; NCOA2; AKT1; JAK2; PIK3R1; CHUK; STAT3; MAP2K1; NFKB1; TGFBR1; ESR1; SMAD4; CEBPB; JUN; AR; AKT3; CCL2; MMP1; STAT1; IL6; HSP90AA1 Axonal Guidance PRKCE; ITGAM; ROCK1; ITGA5; CXCR4; ADAM12; Signaling IGF1; RAC1; RAP1A; EIF4E; PRKCZ; NRP1; NTRK2; ARHGEF7; SMO; ROCK2; MAPK1; PGF; RAC2; PTPN11; GNAS; AKT2; PIK3CA; ERBB2; PRKCI; PTK2; CFL1; GNAQ; PIK3CB; CXCL12; PIK3C3; WNT11; PRKD1; GNB2L1; ABL1; MAPK3; ITGA1; KRAS; RHOA; PRKCD; PIK3C2A; ITGB7; GLI2; PXN; VASP; RAF1; FYN; ITGB1; MAP2K2; PAK4; ADAM17; AKT1; PIK3R1; GLI1; WNT5A; ADAM10; MAP2K1; PAK3; ITGB3; CDC42; VEGFA; ITGA2; EPHA8; CRKL; RND1; GSK3B; AKT3; PRKCA Ephrin Receptor PRKCE; ITGAM; ROCK1; ITGA5; CXCR4; IRAK1; Signaling PRKAA2; EIF2AK2; RAC1; RAP1A; GRK6; ROCK2; MAPK1; PGF; RAC2; PTPN11; GNAS; PLK1; AKT2; DOK1; CDK8; CREB1; PTK2; CFL1; GNAQ; MAP3K14; CXCL12; MAPK8; GNB2L1; ABL1; MAPK3; ITGA1; KRAS; RHOA; PRKCD; PRKAA1; MAPK9; SRC; CDK2; PIM1; ITGB7; PXN; RAF1; FYN; DYRK1A; ITGB1; MAP2K2; PAK4; AKT1; JAK2; STAT3; ADAM10; MAP2K1; PAK3; ITGB3; CDC42; VEGFA; ITGA2; EPHA8; TTK; CSNK1A1; CRKL; BRAF; PTPN13; ATF4; AKT3; SGK Actin Cytoskeleton ACTN4; PRKCE; ITGAM; ROCK1; ITGA5; IRAK1; Signaling PRKAA2; EIF2AK2; RAC1; INS; ARHGEF7; GRK6; ROCK2; MAPK1; RAC2; PLK1; AKT2; PIK3CA; CDK8; PTK2; CFL1; PIK3CB; MYH9; DIAPH1; PIK3C3; MAPK8; F2R; MAPK3; SLC9A1; ITGA1; KRAS; RHOA; PRKCD; PRKAA1; MAPK9; CDK2; PIM1; PIK3C2A; ITGB7; PPP1CC; PXN; VIL2; RAF1; GSN; DYRK1A; ITGB1; MAP2K2; PAK4; PIP5K1A; PIK3R1; MAP2K1; PAK3; ITGB3; CDC42; APC; ITGA2; TTK; CSNK1A1; CRKL; BRAF; VAV3; SGK Huntington's Disease PRKCE; IGF1; EP300; RCOR1; PRKCZ; HDAC4; TGM2; Signaling MAPK1; CAPNS1; AKT2; EGFR; NCOR2; SP1; CAPN2; PIK3CA; HDAC5; CREB1; PRKCI; HSPA5; REST; GNAQ; PIK3CB; PIK3C3; MAPK8; IGF1R; PRKD1; GNB2L1; BCL2L1; CAPN1; MAPK3; CASP8; HDAC2; HDAC7A; PRKCD; HDAC11; MAPK9; HDAC9; PIK3C2A; HDAC3; TP53; CASP9; CREBBP; AKT1; PIK3R1; PDPK1; CASP1; APAF1; FRAP1; CASP2; JUN; BAX; ATF4; AKT3; PRKCA; CLTC; SGK; HDAC6; CASP3 Apoptosis Signaling PRKCE; ROCK1; BID; IRAK1; PRKAA2; EIF2AK2; BAK1; BIRC4; GRK6; MAPK1; CAPNS1; PLK1; AKT2; IKBKB; CAPN2; CDK8; FAS; NFKB2; BCL2; MAP3K14; MAPK8; BCL2L1; CAPN1; MAPK3; CASP8; KRAS; RELA; PRKCD; PRKAA1; MAPK9; CDK2; PIM1; TP53; TNF; RAF1; IKBKG; RELB; CASP9; DYRK1A; MAP2K2; CHUK; APAF1; MAP2K1; NFKB1; PAK3; LMNA; CASP2; BIRC2; TTK; CSNK1A1; BRAF; BAX; PRKCA; SGK; CASP3; BIRC3; PARP1 B Cell Receptor RAC1; PTEN; LYN; ELK1; MAPK1; RAC2; PTPN11; Signaling AKT2; IKBKB; PIK3CA; CREB1; SYK; NFKB2; CAMK2A; MAP3K14; PIK3CB; PIK3C3; MAPK8; BCL2L1; ABL1; MAPK3; ETS1; KRAS; MAPK13; RELA; PTPN6; MAPK9; EGR1; PIK3C2A; BTK; MAPK14; RAF1; IKBKG; RELB; MAP3K7; MAP2K2; AKT1; PIK3R1; CHUK; MAP2K1; NFKB1; CDC42; GSK3A; FRAP1; BCL6; BCL10; JUN; GSK3B; ATF4; AKT3; VAV3; RPS6KB1 Leukocyte Extravasation ACTN4; CD44; PRKCE; ITGAM; ROCK1; CXCR4; CYBA; Signaling RAC1; RAP1A; PRKCZ; ROCK2; RAC2; PTPN11; MMP14; PIK3CA; PRKCI; PTK2; PIK3CB; CXCL12; PIK3C3; MAPK8; PRKD1; ABL1; MAPK10; CYBB; MAPK13; RHOA; PRKCD; MAPK9; SRC; PIK3C2A; BTK; MAPK14; NOX1; PXN; VIL2; VASP; ITGB1; MAP2K2; CTNND1; PIK3R1; CTNNB1; CLDN1; CDC42; F11R; ITK; CRKL; VAV3; CTTN; PRKCA; MMP1; MMP9 Integrin Signaling ACTN4; ITGAM; ROCK1; ITGA5; RAC1; PTEN; RAP1A; TLN1; ARHGEF7; MAPK1; RAC2; CAPNS1; AKT2; CAPN2; PIK3CA; PTK2; PIK3CB; PIK3C3; MAPK8; CAV1; CAPN1; ABL1; MAPK3; ITGA1; KRAS; RHOA; SRC; PIK3C2A; ITGB7; PPP1CC; ILK; PXN; VASP; RAF1; FYN; ITGB1; MAP2K2; PAK4; AKT1; PIK3R1; TNK2; MAP2K1; PAK3; ITGB3; CDC42; RND3; ITGA2; CRKL; BRAF; GSK3B; AKT3 Acute Phase Response IRAK1; SOD2; MYD88; TRAF6; ELK1; MAPK1; PTPN11; Signaling AKT2; IKBKB; PIK3CA; FOS; NFKB2; MAP3K14; PIK3CB; MAPK8; RIPK1; MAPK3; IL6ST; KRAS; MAPK13; IL6R; RELA; SOCS1; MAPK9; FTL; NR3C1; TRAF2; SERPINE1; MAPK14; TNF; RAF1; PDK1; IKBKG; RELB; MAP3K7; MAP2K2; AKT1; JAK2; PIK3R1; CHUK; STAT3; MAP2K1; NFKB1; FRAP1; CEBPB; JUN; AKT3; IL1R1; IL6 PTEN Signaling ITGAM; ITGA5; RAC1; PTEN; PRKCZ; BCL2L11; MAPK1; RAC2; AKT2; EGFR; IKBKB; CBL; PIK3CA; CDKN1B; PTK2; NFKB2; BCL2; PIK3CB; BCL2L1; MAPK3; ITGA1; KRAS; ITGB7; ILK; PDGFRB; INSR; RAF1; IKBKG; CASP9; CDKN1A; ITGB1; MAP2K2; AKT1; PIK3R1; CHUK; PDGFRA; PDPK1; MAP2K1; NFKB1; ITGB3; CDC42; CCND1; GSK3A; ITGA2; GSK3B; AKT3; FOXO1; CASP3; RPS6KB1 p53 Signaling PTEN; EP300; BBC3; PCAF; FASN; BRCA1; GADD45A; BIRC5; AKT2; PIK3CA; CHEK1; TP53INP1; BCL2; PIK3CB; PIK3C3; MAPK8; THBS1; ATR; BCL2L1; E2F1; PMAIP1; CHEK2; TNFRSF10B; TP73; RB1; HDAC9; CDK2; PIK3C2A; MAPK14; TP53; LRDD; CDKN1A; HIPK2; AKT1; PIK3R1; RRM2B; APAF1; CTNNB1; SIRT1; CCND1; PRKDC; ATM; SFN; CDKN2A; JUN; SNAI2; GSK3B; BAX; AKT3 Aryl Hydrocarbon HSPB1; EP300; FASN; TGM2; RXRA; MAPK1; NQO1; Receptor Signaling NCOR2; SP1; ARNT; CDKN1B; FOS; CHEK1; SMARCA4; NFKB2; MAPK8; ALDH1A1; ATR; E2F1; MAPK3; NRIP1; CHEK2; RELA; TP73; GSTP1; RB1; SRC; CDK2; AHR; NFE2L2; NCOA3; TP53; TNF; CDKN1A; NCOA2; APAF1; NFKB1; CCND1; ATM; ESR1; CDKN2A; MYC; JUN; ESR2; BAX; IL6; CYP1B1; HSP90AA1 Xenobiotic Metabolism PRKCE; EP300; PRKCZ; RXRA; MAPK1; NQO1; Signaling NCOR2; PIK3CA; ARNT; PRKCI; NFKB2; CAMK2A; PIK3CB; PPP2R1A; PIK3C3; MAPK8; PRKD1; ALDH1A1; MAPK3; NRIP1; KRAS; MAPK13; PRKCD; GSTP1; MAPK9; NOS2A; ABCB1; AHR; PPP2CA; FTL; NFE2L2; PIK3C2A; PPARGC1A; MAPK14; TNF; RAF1; CREBBP; MAP2K2; PIK3R1; PPP2R5C; MAP2K1; NFKB1; KEAP1; PRKCA; EIF2AK3; IL6; CYP1B1; HSP90AA1 SAPK/JNK Signaling PRKCE; IRAK1; PRKAA2; EIF2AK2; RAC1; ELK1; GRK6; MAPK1; GADD45A; RAC2; PLK1; AKT2; PIK3CA; FADD; CDK8; PIK3CB; PIK3C3; MAPK8; RIPK1; GNB2L1; IRS1; MAPK3; MAPK10; DAXX; KRAS; PRKCD; PRKAA1; MAPK9; CDK2; PIM1; PIK3C2A; TRAF2; TP53; LCK; MAP3K7; DYRK1A; MAP2K2; PIK3R1; MAP2K1; PAK3; CDC42; JUN; TTK; CSNK1A1; CRKL; BRAF; SGK PPAr/RXR Signaling PRKAA2; EP300; INS; SMAD2; TRAF6; PPARA; FASN; RXRA; MAPK1; SMAD3; GNAS; IKBKB; NCOR2; ABCA1; GNAQ; NFKB2; MAP3K14; STAT5B; MAPK8; IRS1; MAPK3; KRAS; RELA; PRKAA1; PPARGC1A; NCOA3; MAPK14; INSR; RAF1; IKBKG; RELB; MAP3K7; CREBBP; MAP2K2; JAK2; CHUK; MAP2K1; NFKB1; TGFBR1; SMAD4; JUN; IL1R1; PRKCA; IL6; HSP90AA1; ADIPOQ NF-KB Signaling IRAK1; EIF2AK2; EP300; INS; MYD88; PRKCZ; TRAF6; TBK1; AKT2; EGFR; IKBKB; PIK3CA; BTRC; NFKB2; MAP3K14; PIK3CB; PIK3C3; MAPK8; RIPK1; HDAC2; KRAS; RELA; PIK3C2A; TRAF2; TLR4; PDGFRB; TNF; INSR; LCK; IKBKG; RELB; MAP3K7; CREBBP; AKT1; PIK3R1; CHUK; PDGFRA; NFKB1; TLR2; BCL10; GSK3B; AKT3; TNFAIP3; IL1R1 Neuregulin Signaling ERBB4; PRKCE; ITGAM; ITGA5; PTEN; PRKCZ; ELK1; MAPK1; PTPN11; AKT2; EGFR; ERBB2; PRKCI; CDKN1B; STAT5B; PRKD1; MAPK3; ITGA1; KRAS; PRKCD; STAT5A; SRC; ITGB7; RAF1; ITGB1; MAP2K2; ADAM17; AKT1; PIK3R1; PDPK1; MAP2K1; ITGB3; EREG; FRAP1; PSEN1; ITGA2; MYC; NRG1; CRKL; AKT3; PRKCA; HSP90AA1; RPS6KB1 Wnt & Beta catenin CD44; EP300; LRP6; DVL3; CSNK1E; GJA1; SMO; Signaling AKT2; PIN1; CDH1; BTRC; GNAQ; MARK2; PPP2R1A; WNT11; SRC; DKK1; PPP2CA; SOX6; SFRP2; ILK; LEF1; SOX9; TP53; MAP3K7; CREBBP; TCF7L2; AKT1; PPP2R5C; WNT5A; LRP5; CTNNB1; TGFBR1; CCND1; GSK3A; DVL1; APC; CDKN2A; MYC; CSNK1A1; GSK3B; AKT3; SOX2 Insulin Receptor PTEN; INS; EIF4E; PTPN1; PRKCZ; MAPK1; TSC1; Signaling PTPN11; AKT2; CBL; PIK3CA; PRKCI; PIK3CB; PIK3C3; MAPK8; IRS1; MAPK3; TSC2; KRAS; EIF4EBP1; SLC2A4; PIK3C2A; PPP1CC; INSR; RAF1; FYN; MAP2K2; JAK1; AKT1; JAK2; PIK3R1; PDPK1; MAP2K1; GSK3A; FRAP1; CRKL; GSK3B; AKT3; FOXO1; SGK; RPS6KB1 IL-6 Signaling HSPB1; TRAF6; MAPKAPK2; ELK1; MAPK1; PTPN11; IKBKB; FOS; NFKB2; MAP3K14; MAPK8; MAPK3; MAPK10; IL6ST; KRAS; MAPK13; IL6R; RELA; SOCS1; MAPK9; ABCB1; TRAF2; MAPK14; TNF; RAF1; IKBKG; RELB; MAP3K7; MAP2K2; IL8; JAK2; CHUK; STAT3; MAP2K1; NFKB1; CEBPB; JUN; IL1R1; SRF; IL6 Hepatic Cholestasis PRKCE; IRAK1; INS; MYD88; PRKCZ; TRAF6; PPARA; RXRA; IKBKB; PRKCI; NFKB2; MAP3K14; MAPK8; PRKD1; MAPK10; RELA; PRKCD; MAPK9; ABCB1; TRAF2; TLR4; TNF; INSR; IKBKG; RELB; MAP3K7; IL8; CHUK; NR1H2; TJP2; NFKB1; ESR1; SREBF1; FGFR4; JUN; IL1R1; PRKCA; IL6 IGF-1 Signaling IGF1; PRKCZ; ELK1; MAPK1; PTPN11; NEDD4; AKT2; PIK3CA; PRKCI; PTK2; FOS; PIK3CB; PIK3C3; MAPK8; IGF1R; IRS1; MAPK3; IGFBP7; KRAS; PIK3C2A; YWHAZ; PXN; RAF1; CASP9; MAP2K2; AKT1; PIK3R1; PDPK1; MAP2K1; IGFBP2; SFN; JUN; CYR61; AKT3; FOXO1; SRF; CTGF; RPS6KB1 NRF2-mediated PRKCE; EP300; SOD2; PRKCZ; MAPK1; SQSTM1; Oxidative Stress Response NQO1; PIK3CA; PRKCI; FOS; PIK3CB; PIK3C3; MAPK8; PRKD1; MAPK3; KRAS; PRKCD; GSTP1; MAPK9; FTL; NFE2L2; PIK3C2A; MAPK14; RAF1; MAP3K7; CREBBP; MAP2K2; AKT1; PIK3R1; MAP2K1, PPIB; JUN; KEAP1; GSK3B; ATF4; PRKCA; EIF2AK3; HSP90AA1 Hepatic Fibrosis/Hepatic EDN1; IGF1; KDR; FLT1; SMAD2; FGFR1; MET; PGF; Stellate Cell Activation SMAD3; EGFR; FAS; CSF1; NFKB2; BCL2; MYH9; IGF1R; IL6R; RELA; TLR4; PDGFRB; TNF; RELB; IL8; PDGFRA; NFKB1; TGFBR1; SMAD4; VEGFA; BAX; IL1R1; CCL2; HGF; MMP1; STAT1; IL6; CTGF; MMP9 PPAR Signaling EP300; INS; TRAF6; PPARA; RXRA; MAPK1; IKBKB; NCOR2; FOS; NFKB2; MAP3K14; STAT5B; MAPK3; NRIP1; KRAS; PPARG; RELA; STAT5A; TRAF2; PPARGC1A; PDGFRB; TNF; INSR; RAF1; IKBKG; RELB; MAP3K7; CREBBP; MAP2K2; CHUK; PDGFRA; MAP2K1; NFKB1; JUN; IL1R1; HSP90AA1 Fc Epsilon RI Signaling PRKCE; RAC1; PRKCZ; LYN; MAPK1; RAC2; PTPN11; AKT2; PIK3CA; SYK; PRKCI; PIK3CB; PIK3C3; MAPK8; PRKD1; MAPK3; MAPK10; KRAS; MAPK13; PRKCD; MAPK9; PIK3C2A; BTK; MAPK14; TNF; RAF1; FYN; MAP2K2; AKT1; PIK3R1; PDPK1; MAP2K1; AKT3; VAV3; PRKCA G-Protein Coupled PRKCE; RAP1A; RGS16; MAPK1; GNAS; AKT2; IKBKB; Receptor Signaling PIK3CA; CREB1; GNAQ; NFKB2; CAMK2A; PIK3CB; PIK3C3; MAPK3; KRAS; RELA; SRC; PIK3C2A; RAF1; IKBKG; RELB; FYN; MAP2K2; AKT1; PIK3R1; CHUK; PDPK1; STAT3; MAP2K1; NFKB1; BRAF; ATF4; AKT3; PRKCA Inositol Phosphate PRKCE; IRAK1; PRKAA2; EIF2AK2; PTEN; GRK6; Metabolism MAPK1; PLK1; AKT2; PIK3CA; CDK8; PIK3CB; PIK3C3; MAPK8; MAPK3; PRKCD; PRKAA1; MAPK9; CDK2; PIM1; PIK3C2A; DYRK1A; MAP2K2; PIP5K1A; PIK3R1; MAP2K1; PAK3; ATM; TTK; CSNK1A1; BRAF; SGK PDGF Signaling EIF2AK2; ELK1; ABL2; MAPK1; PIK3CA; FOS; PIK3CB; PIK3C3; MAPK8; CAV1; ABL1; MAPK3; KRAS; SRC; PIK3C2A; PDGFRB; RAF1; MAP2K2; JAK1; JAK2; PIK3R1; PDGFRA; STAT3; SPHK1; MAP2K1; MYC; JUN; CRKL; PRKCA; SRF; STAT1; SPHK2 VEGF Signaling ACTN4; ROCK1; KDR; FLT1; ROCK2; MAPK1; PGF; AKT2; PIK3CA; ARNT; PTK2; BCL2; PIK3CB; PIK3C3; BCL2L1; MAPK3; KRAS; HIF1A; NOS3; PIK3C2A; PXN; RAF1; MAP2K2; ELAVL1; AKT1; PIK3R1; MAP2K1; SFN; VEGFA; AKT3; FOXO1; PRKCA Natural Killer Cell PRKCE; RAC1; PRKCZ; MAPK1; RAC2; PTPN11; Signaling KIR2DL3; AKT2; PIK3CA; SYK; PRKCI; PIK3CB; PIK3C3; PRKD1; MAPK3; KRAS; PRKCD; PTPN6; PIK3C2A; LCK; RAF1; FYN; MAP2K2; PAK4; AKT1; PIK3R1; MAP2K1; PAK3; AKT3; VAV3; PRKCA Cell Cycle: G1/S HDAC4; SMAD3; SUV39H1; HDAC5; CDKN1B; BTRC; Checkpoint Regulation ATR; ABL1; E2F1; HDAC2; HDAC7A; RB1; HDAC11; HDAC9; CDK2; E2F2; HDAC3; TP53; CDKN1A; CCND1; E2F4; ATM; RBL2; SMAD4; CDKN2A; MYC; NRG1; GSK3B; RBL1; HDAC6 T Cell Receptor RAC1; ELK1; MAPK1; IKBKB; CBL; PIK3CA; FOS; Signaling NFKB2; PIK3CB; PIK3C3; MAPK8; MAPK3; KRAS; RELA; PIK3C2A; BTK; LCK; RAF1; IKBKG; RELB; FYN; MAP2K2; PIK3R1; CHUK; MAP2K1; NFKB1; ITK; BCL10; JUN; VAV3 Death Receptor Signaling CRADD; HSPB1; BID; BIRC4; TBK1; IKBKB; FADD; FAS; NFKB2; BCL2; MAP3K14; MAPK8; RIPK1; CASP8; DAXX; TNFRSF10B; RELA; TRAF2; TNF; IKBKG; RELB; CASP9; CHUK; APAF1; NFKB1; CASP2; BIRC2; CASP3; BIRC3 FGF Signaling RAC1; FGFR1; MET; MAPKAPK2; MAPK1; PTPN11; AKT2; PIK3CA; CREB1; PIK3CB; PIK3C3; MAPK8; MAPK3; MAPK13; PTPN6; PIK3C2A; MAPK14; RAF1; AKT1; PIK3R1; STAT3; MAP2K1; FGFR4; CRKL; ATF4; AKT3; PRKCA; HGF GM-CSF Signaling LYN; ELK1; MAPK1; PTPN11; AKT2; PIK3CA; CAMK2A; STAT5B; PIK3CB; PIK3C3; GNB2L1; BCL2L1; MAPK3; ETS1; KRAS; RUNX1; PIM1; PIK3C2A; RAF1; MAP2K2; AKT1; JAK2; PIK3R1; STAT3; MAP2K1; CCND1; AKT3; STAT1 Amyotrophic Lateral BID; IGF1; RAC1; BIRC4; PGF; CAPNS1; CAPN2; Sclerosis Signaling PIK3CA; BCL2; PIK3CB; PIK3C3; BCL2L1; CAPN1; PIK3C2A; TP53; CASP9; PIK3R1; RAB5A; CASP1; APAF1; VEGFA; BIRC2; BAX; AKT3; CASP3; BIRC3 JAK/Stat Signaling PTPN1; MAPK1; PTPN11; AKT2; PIK3CA; STAT5B; PIK3CB; PIK3C3; MAPK3; KRAS; SOCS1; STAT5A; PTPN6; PIK3C2A; RAF1; CDKN1A; MAP2K2; JAK1; AKT1; JAK2; PIK3R1; STAT3; MAP2K1; FRAP1; AKT3; STAT1 Nicotinate and PRKCE; IRAK1; PRKAA2; EIF2AK2; GRK6; MAPK1; Nicotinamide Metabolism PLK1; AKT2; CDK8; MAPK8; MAPK3; PRKCD; PRKAA1; PBEF1; MAPK9; CDK2; PIM1; DYRK1A; MAP2K2; MAP2K1; PAK3; NT5E; TTK; CSNK1A1; BRAF; SGK Chemokine Signaling CXCR4; ROCK2; MAPK1; PTK2; FOS; CFL1; GNAQ; CAMK2A; CXCL12; MAPK8; MAPK3; KRAS; MAPK13; RHOA; CCR3; SRC; PPP1CC; MAPK14; NOX1; RAF1; MAP2K2; MAP2K1; JUN; CCL2; PRKCA IL-2 Signaling ELK1; MAPK1; PTPN11; AKT2; PIK3CA; SYK; FOS; STAT5B; PIK3CB; PIK3C3; MAPK8; MAPK3; KRAS; SOCS1; STAT5A; PIK3C2A; LCK; RAF1; MAP2K2; JAK1; AKT1; PIK3R1; MAP2K1; JUN; AKT3 Synaptic Long Term PRKCE; IGF1; PRKCZ; PRDX6; LYN; MAPK1; GNAS; Depression PRKCI; GNAQ; PPP2R1A; IGF1R; PRKD1; MAPK3; KRAS; GRN; PRKCD; NOS3; NOS2A; PPP2CA; YWHAZ; RAF1; MAP2K2; PPP2R5C; MAP2K1; PRKCA Estrogen Receptor TAF4B; EP300; CARM1; PCAF; MAPK1; NCOR2; Signaling SMARCA4; MAPK3; NRIP1; KRAS; SRC; NR3C1; HDAC3; PPARGC1A; RBM9; NCOA3; RAF1; CREBBP; MAP2K2; NCOA2; MAP2K1; PRKDC; ESR1; ESR2 Protein Ubiquitination TRAF6; SMURF1; BIRC4; BRCA1; UCHL1; NEDD4; Pathway CBL; UBE2I; BTRC; HSPA5; USP7; USP10; FBW7; USP9X; STUB1; USP22; B2M; BIRC2; PARK2; USP8; USP1; VHL; HSP90AA1; BIRC3 IL-10 Signaling TRAF6; CCR1; ELK1; IKBKB; SP1; FOS; NFKB2; MAP3K14; MAPK8; MAPK13; RELA; MAPK14; TNF; IKBKG; RELB; MAP3K7; JAK1; CHUK; STAT3; NFKB1; JUN; IL1R1; IL6 VDR/RXR Activation PRKCE; EP300; PRKCZ; RXRA; GADD45A; HES1; NCOR2; SP1; PRKCI; CDKN1B; PRKD1; PRKCD; RUNX2; KLF4; YY1; NCOA3; CDKN1A; NCOA2; SPP1; LRP5; CEBPB; FOXO1; PRKCA TGF-beta Signaling EP300; SMAD2; SMURF1; MAPK1; SMAD3; SMAD1; FOS; MAPK8; MAPK3; KRAS; MAPK9; RUNX2; SERPINE1; RAF1; MAP3K7; CREBBP; MAP2K2; MAP2K1; TGFBR1; SMAD4; JUN; SMAD5 Toll-like Receptor IRAK1; EIF2AK2; MYD88; TRAF6; PPARA; ELK1; Signaling IKBKB; FOS; NFKB2; MAP3K14; MAPK8; MAPK13; RELA; TLR4; MAPK14; IKBKG; RELB; MAP3K7; CHUK; NFKB1; TLR2; JUN p38 MAPK Signaling HSPB1; IRAK1; TRAF6; MAPKAPK2; ELK1; FADD; FAS; CREB1; DDIT3; RPS6KA4; DAXX; MAPK13; TRAF2; MAPK14; TNF; MAP3K7; TGFBR1; MYC; ATF4; IL1R1; SRF; STAT1 Neurotrophin/TRK NTRK2; MAPK1; PTPN11; PIK3CA; CREB1; FOS; Signaling PIK3CB; PIK3C3; MAPK8; MAPK3; KRAS; PIK3C2A; RAF1; MAP2K2; AKT1; PIK3R1; PDPK1; MAP2K1; CDC42; JUN; ATF4 FXR/RXR Activation INS; PPARA; FASN; RXRA; AKT2; SDC1; MAPK8; APOB; MAPK10; PPARG; MTTP; MAPK9; PPARGC1A; TNF; CREBBP; AKT1; SREBF1; FGFR4; AKT3; FOXO1 Synaptic Long Term PRKCE; RAP1A; EP300; PRKCZ; MAPK1; CREB1; Potentiation PRKCI; GNAQ; CAM1K2A; PRKD1; MAPK3; KRAS; PRKCD; PPP1CC; RAF1; CREBBP; MAP2K2; MAP2K1; ATF4; PRKCA Calcium Signaling RAP1A; EP300; HDAC4; MAPK1; HDAC5; CREB1; CAMK2A; MYH9; MAPK3; HDAC2; HDAC7A; HDAC11; HDAC9; HDAC3; CREBBP; CALR; CAMKK2; ATF4; HDAC6 EGF Signaling ELK1; MAPK1; EGFR; PIK3CA; FOS; PIK3CB; PIK3C3; MAPK8; MAPK3; PIK3C2A, RAF1; JAK1; PIK3R1; STAT3; MAP2K1; JUN; PRKCA; SRF; STAT1 Hypoxia Signaling in the EDN1; PTEN; EP300; NQO1; UBE2I; CREB1; ARNT; Cardiovascular System HIF1A; SLC2A4; NOS3; TP53; LDHA; AKT1; ATM; VEGFA; JUN; ATF4; VHL; HSP90AA1 LPS/IL-1 Mediated IRAK1; MYD88; TRAF6; PPARA; RXRA; ABCA1; Inhibition of RXR Function MAPK8; ALDH1A1; GSTP1; MAPK9; ABCB1; TRAF2; TLR4; TNF; MAP3K7; NR1H2; SREBF1; JUN; IL1R1 LXR/RXR Activation FASN; RXRA; NCOR2; ABCA1; NFKB2; IRF3; RELA; NOS2A; TLR4; TNF; RELB; LDLR; NR1H2; NFKB1; SREBF1; IL1R1; CCL2; IL6; MMP9 Amyloid Processing PRKCE; CSNK1E; MAPK1; CAPNS1; AKT2; CAPN2; CAPN1; MAPK3; MAPK13; MAPT; MAPK14; AKT1; PSEN1; CSNK1A1; GSK3B; AKT3; APP IL-4 Signaling AKT2; PIK3CA; PIK3CB; PIK3C3; IRS1; KRAS; SOCS1; PTPN6; NR3C1; PIK3C2A; JAK1; AKT1; JAK2; PIK3R1; FRAP1; AKT3; RPS6KB1 Cell Cycle: G2/M DNA EP300; PCAF; BRCA1; GADD45A; PLK1; BTRC; Damage Checkpoint CHEK1; ATR; CHEK2; YWHAZ; TP53; CDKN1A; Regulation PRKDC; ATM; SFN; CDKN2A Nitric Oxide Signaling in KDR; FLT1; PGF; AKT2; PIK3CA; PIK3CB; PIK3C3; the Cardiovascular System CAV1; PRKCD; NOS3; PIK3C2A; AKT1; PIK3R1; VEGFA; AKT3; HSP90AA1 Purine Metabolism NME2; SMARCA4; MYH9; RRM2; ADAR; EIF2AK4; PKM2; ENTPD1; RAD51; RRM2B; TJP2; RAD51C; NT5E; POLD1; NME1 cAMP-mediated RAP1A; MAPK1; GNAS; CREB1; CAMK2A; MAPK3; Signaling SRC; RAF1; MAP2K2; STAT3; MAP2K1; BRAF; ATF4 Mitochondrial SOD2; MAPK8; CASP8; MAPK10; MAPK9; CASP9; Dysfunction PARK7; PSEN1; PARK2; APP; CASP3 Notch Signaling HES1; JAG1; NUMB; NOTCH4; ADAM17; NOTCH2; PSEN1; NOTCH3; NOTCH1; DLL4 Endoplasmic Reticulum HSPA5; MAPK8; XBP1; TRAF2; ATF6; CASP9; ATF4; Stress Pathway EIF2AK3; CASP3 Pyrimidine Metabolism NME2; AICDA; RRM2; EIF2AK4; ENTPD1; RRM2B; NT5E; POLD1; NME1 Parkinson's Signaling UCHL1; MAPK8; MAPK13; MAPK14; CASP9; PARK7; PARK2; CASP3 Cardiac & Beta GNAS; GNAQ; PPP2R1A; GNB2L1; PPP2CA; PPP1CC; Adrenergic Signaling PPP2R5C Glycolysis/Gluconeogenesis HK2; GCK; GPI; ALDH1A1; PKM2; LDHA; HK1 Interferon Signaling IRF1; SOCS1; JAK1; JAK2; IFITM1; STAT1; IFIT3 Sonic Hedgehog ARRB2; SMO; GLI2; DYRK1A; GLI1; GSK3B; DYRK1B Signaling Glycerophospholipid PLD1; GRN; GPAM; YWHAZ; SPHK1; SPHK2 Metabolism Phospholipid PRDX6; PLD1; GRN; YWHAZ; SPHK1; SPHK2 Degradation Tryptophan Metabolism SIAH2; PRMT5; NEDD4; ALDH1A1; CYP1B1; SIAH1 Lysine Degradation SUV39H1; EHMT2; NSD1; SETD7; PPP2R5C Nucleotide Excision ERCC5; ERCC4; XPA; XPC; ERCC1 Repair Pathway Starch and Sucrose UCHL1; HK2; GCK; GPI; HK1 Metabolism Aminosugars Metabolism NQO1; HK2; GCK; HK1 Arachidonic Acid PRDX6; GRN; YWHAZ; CYP1B1 Metabolism Circadian Rhythm CSNK1E; CREB1; ATF4; NR1D1 Signaling Coagulation System BDKRB1; F2R; SERPINE1; F3 Dopamine Receptor PPP2R1A; PPP2CA; PPP1CC; PPP2R5C Signaling Glutathione Metabolism IDH2; GSTP1; ANPEP; IDH1 Glycerolipid Metabolism ALDH1A1; GPAM; SPHK1; SPHK2 Linoleic Acid PRDX6; GRN; YWHAZ; CYP1B1 Metabolism Methionine Metabolism DNMT1; DNWIT3B; AHCY; DNMT3A Pyruvate Metabolism GLO1; ALDH1A1; PKM2; LDHA Arginine and Proline ALDH1A1; NOS3; NOS2A Metabolism Eicosanoid Signaling PRDX6; GRN; YWHAZ Fructose and Mannose HK2; GCK; HK1 Metabolism Galactose Metabolism HK2; GCK; HK1 Stilbene, Coumarine and PRDX6; PRDX1; TYR Lignin Biosynthesis Antigen Presentation CALR; B2M Pathway Biosynthesis of Steroids NQO1; DHCR7 Butanoate Metabolism ALDH1A1; NLGN1 Citrate Cycle IDH2; IDH1 Fatty Acid Metabolism ALDH1A1; CYP1B1 Glycerophospholipid PRDX6; CHKA Metabolism Histidine Metabolism PRMT5; ALDH1A1 Inositol Metabolism ERO1L; APEX1 Metabolism of GSTP1; CYP1B1 Xenobiotics by Cytochrome p450 Methane Metabolism PRDX6; PRDX1 Phenylalanine PRDX6; PRDX1 Metabolism Propanoate Metabolism ALDH1A1; LDHA Selenoamino Acid PRMT5; AHCY Metabolism Sphingolipid Metabolism SPHK1; SPHK2 Aminophosphonate PRMT5 Metabolism Androgen and Estrogen PRMT5 Metabolism Ascorbate and Aldarate ALDH1A1 Metabolism Bile Acid Biosynthesis ALDH1A1 Cysteine Metabolism LDHA Fatty Acid Biosynthesis FASN Glutamate Receptor GNB2L1 Signaling NRF2-mediated PRDX1 Oxidative Stress Response Pentose Phosphate GPI Pathway Pentose and Glucuronate UCHL1 Interconversions Retinol Metabolism ALDH1A1 Riboflavin Metabolism TYR Tyrosine Metabolism PRMT5, TYR Ubiquinone Biosynthesis PRMT5 Valine, Leucine and ALDH1A1 Isoleucine Degradation Glycine, Serine and CHKA Threonine Metabolism Lysine Degradation ALDH1A1 Pain/Taste TRPM5; TRPA1 Pain TRPM7; TRPC5; TRPC6; TRPC1; Cnr1; cnr2; Grk2; Trpa1; Pomc; Cgrp; Crf; Pka; Era; Nr2b; TRPM5; Prkaca; Prkacb; Prkar1a; Prkar2a Mitochondrial Function AIF; CytC; SMAC (Diablo); Aifm-1; Aifm-2 Developmental BMP-4; Chordin (Chrd); Noggin (Nog); WNT (Wnt2; Neurology Wnt2b; Wnt3a; Wnt4; Wnt5a; Wnt6; Wnt7b; Wnt8b; Wnt9a; Wnt9b; Wnt10a; Wnt10b; Wnt16); beta-catenin; Dkk-1; Frizzled related proteins; Otx-2; Gbx2; FGF-8; Reelin; Dab1; unc-86 (Pou4f1 or Brn3a); Numb; Reln

Embodiments of the invention also relate to methods and compositions related to knocking out genes, amplifying genes and repairing particular mutations associated with DNA repeat instability and neurological disorders (Robert D. Wells, Tetsuo Ashizawa, Genetic Instabilities and Neurological Diseases, Second Edition, Academic Press, Oct. 13, 2011—Medical). Specific aspects of tandem repeat sequences have been found to be responsible for more than twenty human diseases (New insights into repeat instability: role of RNA•DNA hybrids. McIvor E I, Polak U, Napierala M. RNA Biol. 2010 September-October; 7(5):551-8). The CRISPR-Cas system may be harnessed to correct these defects of genomic instability.

A further aspect of the invention relates to utilizing the CRISPR-Cas system for correcting defects in the EMP2A and EMP2B genes that have been identified to be associated with Lafora disease. Lafora disease is an autosomal recessive condition which is characterized by progressive myoclonus epilepsy which may start as epileptic seizures in adolescence. A few cases of the disease may be caused by mutations in genes yet to be identified. The disease causes seizures, muscle spasms, difficulty walking, dementia, and eventually death. There is currently no therapy that has proven effective against disease progression. Other genetic abnormalities associated with epilepsy may also be targeted by the CRISPR-Cas system and the underlying genetics is further described in Genetics of Epilepsy and Genetic Epilepsies, edited by Giuliano Avanzini, Jeffrey L. Noebels, Mariani Foundation Paediatric Neurology:20; 2009).

In yet another aspect of the invention, the CRISPR-Cas system may be used to correct ocular defects that arise from several genetic mutations further described in Genetic Diseases of the Eye, Second Edition, edited by Elias I. Traboulsi, Oxford University Press, 2012.

Several further aspects of the invention relate to correcting defects associated with a wide range of genetic diseases which are further described on the website of the National Institutes of Health under the topic subsection Genetic Disorders (website at health.nih.gov/topic/GeneticDisorders). The genetic brain diseases may include but are not limited to Adrenoleukodystrophy, Agenesis of the Corpus Callosum, Aicardi Syndrome, Alpers'

Disease, Alzheimer's Disease, Barth Syndrome, Batten Disease, CADASIL, Cerebellar Degeneration, Fabry's Disease, Gerstmann-Straussler-Scheinker Disease, Huntington's Disease and other Triplet Repeat Disorders, Leigh's Disease, Lesch-Nyhan Syndrome, Menkes Disease, Mitochondrial Myopathies and NINDS Colpocephaly. These diseases are further described on the website of the National Institutes of Health under the subsection Genetic Brain Disorders.

In some embodiments, the condition may be neoplasia. In some embodiments, where the condition is neoplasia, the genes to be targeted are any of those listed in Table A (in this case PTEN asn so forth). In some embodiments, the condition may be Age-related Macular Degeneration. In some embodiments, the condition may be a Schizophrenic Disorder. In some embodiments, the condition may be a Trinucleotide Repeat Disorder. In some embodiments, the condition may be Fragile X Syndrome. In some embodiments, the condition may be a Secretase Related Disorder. In some embodiments, the condition may be a Prion-related disorder. In some embodiments, the condition may be ALS. In some embodiments, the condition may be a drug addiction. In some embodiments, the condition may be Autism. In some embodiments, the condition may be Alzheimer's Disease. In some embodiments, the condition may be inflammation. In some embodiments, the condition may be Parkinson's Disease.

Examples of proteins associated with Parkinson's disease include but are not limited to α-synuclein, DJ-1, LRRK2, PINK1, Parkin, UCHL1, Synphilin-1, and NURR1. Examples of addiction-related proteins may include ABAT for example.

Examples of inflammation-related proteins may include the monocyte chemoattractant protein-1 (MCP1) encoded by the Ccr2 gene, the C-C chemokine receptor type 5 (CCR5) encoded by the Ccr5 gene, the IgG receptor IIB (FCGR2b, also termed CD32) encoded by the Fcgr2b gene, or the Fc epsilon R1g (FCER1g) protein encoded by the Fcer1g gene, for example.

Examples of cardiovascular diseases associated proteins may include IL1B (interleukin 1, beta), XDH (xanthine dehydrogenase), TP53 (tumor protein p53), PTGIS (prostaglandin 12 (prostacyclin) synthase), MB (myoglobin), IL4 (interleukin 4), ANGPT1 (angiopoietin 1), ABCG8 (ATP-binding cassette, sub-family G (WHITE), member 8), or CTSK (cathepsin K), for example.

Examples of Alzheimer's disease associated proteins may include the very low density lipoprotein receptor protein (VLDLR) encoded by the VLDLR gene, the ubiquitin-like modifier activating enzyme 1 (UBA1) encoded by the UBA1 gene, or the NEDD8-activating enzyme E1 catalytic subunit protein (UBE1C) encoded by the UBA3 gene, for example.

Examples of proteins associated Autism Spectrum Disorder may include the benzodiazapine receptor (peripheral) associated protein 1 (BZRAP1) encoded by the BZRAP1 gene, the AF4/FMR2 family member 2 protein (AFF2) encoded by the AFF2 gene (also termed MFR2), the fragile X mental retardation autosomal homolog 1 protein (FXR1) encoded by the FXR1 gene, or the fragile X mental retardation autosomal homolog 2 protein (FXR2) encoded by the FXR2 gene, for example.

Examples of proteins associated Macular Degeneration may include the ATP-binding cassette, sub-family A (ABC1) member 4 protein (ABCA4) encoded by the ABCR gene, the apolipoprotein E protein (APOE) encoded by the APOE gene, or the chemokine (C-C motif) Ligand 2 protein (CCL2) encoded by the CCL2 gene, for example.

Examples of proteins associated Schizophrenia may include NRG1, ErbB4, CPLX1, TPH1, TPH2, NRXN1, GSK3A, BDNF, DISC1, GSK3B, and combinations thereof.

Examples of proteins involved in tumor suppression may include ATM (ataxia telangiectasia mutated), ATR (ataxia telangiectasia and Rad3 related), EGFR (epidermal growth factor receptor), ERBB2 (v-erb-b2 erythroblastic leukemia viral oncogene homolog 2), ERBB3 (v-erb-b2 erythroblastic leukemia viral oncogene homolog 3), ERBB4 (v-erb-b2 erythroblastic leukemia viral oncogene homolog 4), Notch 1, Notch2, Notch 3, or Notch 4, for example.

Examples of proteins associated with a secretase disorder may include PSENEN (presenilin enhancer 2 homolog (C. elegans)), CTSB (cathepsin B), PSEN1 (presenilin 1), APP (amyloid beta (A4) precursor protein), APH1B (anterior pharynx defective 1 homolog B (C. elegans)), PSEN2 (presenilin 2 (Alzheimer disease 4)), or BACE1 (beta-site APP-cleaving enzyme 1), for example.

Examples of proteins associated with Amyotrophic Lateral Sclerosis may include SOD1 (superoxide dismutase 1), ALS2 (amyotrophic lateral sclerosis 2), FUS (fused in sarcoma), TARDBP (TAR DNA binding protein), VAGFA (vascular endothelial growth factor A), VAGFB (vascular endothelial growth factor B), and VAGFC (vascular endothelial growth factor C), and any combination thereof.

Examples of proteins associated with prion diseases may include SOD1 (superoxide dismutase 1), ALS2 (amyotrophic lateral sclerosis 2), FUS (fused in sarcoma), TARDBP (TAR DNA binding protein), VAGFA (vascular endothelial growth factor A), VAGFB (vascular endothelial growth factor B), and VAGFC (vascular endothelial growth factor C), and any combination thereof.

Examples of proteins related to neurodegenerative conditions in prion disorders may include A2M (Alpha-2-Macroglobulin), AATF (Apoptosis antagonizing transcription factor), ACPP (Acid phosphatase prostate), ACTA2 (Actin alpha 2 smooth muscle aorta), ADAM22 (ADAM metallopeptidase domain), ADORA3 (Adenosine A3 receptor), or ADRA1D (Alpha-1D adrenergic receptor for Alpha-1D adrenoreceptor), for example.

Examples of proteins associated with Immunodeficiency may include A2M [alpha-2-macroglobulin]; AANAT [arylalkylamine N-acetyltransferase]; ABCA1 [ATP-binding cassette, sub-family A (ABC1), member 1]; ABCA2 [ATP-binding cassette, sub-family A (ABC1), member 2]; or ABCA3 [ATP-binding cassette, sub-family A (ABC1), member 3]; for example.

Examples of proteins associated with Trinucleotide Repeat Disorders include AR (androgen receptor), FMR1 (fragile X mental retardation 1), HTT (huntingtin), or DMPK (dystrophia myotonica-protein kinase), FXN (frataxin), ATXN2 (ataxin 2), for example.

Examples of proteins associated with Neurotransmission Disorders include SST (somatostatin), NOS1 (nitric oxide synthase 1 (neuronal)), ADRA2A (adrenergic, alpha-2A-, receptor), ADRA2C (adrenergic, alpha-2C-, receptor), TACR1 (tachykinin receptor 1), or HTR2c (5-hydroxytryptamine (serotonin) receptor 2C), for example.

Examples of neurodevelopmental-associated sequences include A2BP1 [ataxin 2-binding protein 1], AADAT [aminoadipate aminotransferase], AANAT [arylalkylamine N-acetyltransferase], ABAT [4-aminobutyrate aminotransferase], ABCA1 [ATP-binding cassette, sub-family A (ABC1), member 1], or ABCA13 [ATP-binding cassette, sub-family A (ABC1), member 13], for example.

Further examples of preferred conditions treatable with the present system include may be selected from: Aicardi-Goutiéres Syndrome; Alexander Disease; Allan-Herndon-Dudley Syndrome; POLG-Related Disorders; Alpha-Mannosidosis (Type II and III); Alström Syndrome; Angelman; Syndrome; Ataxia-Telangiectasia; Neuronal Ceroid-Lipofuscinoses; Beta-Thalassemia; Bilateral Optic Atrophy and (Infantile) Optic Atrophy Type 1; Retinoblastoma (bilateral); Canavan Disease; Cerebrooculofacioskeletal Syndrome 1 [COF S1]; Cerebrotendinous Xanthomatosis; Cornelia de Lange Syndrome; MAPT-Related Disorders; Genetic Prion Diseases; Dravet Syndrome; Early-Onset Familial Alzheimer Disease; Friedreich Ataxia [FRDA]; Fryns Syndrome; Fucosidosis; Fukuyama Congenital Muscular Dystrophy; Galactosialidosis; Gaucher Disease; Organic Acidemias; Hemophagocytic Lymphohistiocytosis; Hutchinson-Gilford Progeria Syndrome; Mucolipidosis II; Infantile Free Sialic Acid Storage Disease; PLA2G6-Associated Neurodegeneration; Jervell and Lange-Nielsen Syndrome; Junctional Epidermolysis Bullosa; Huntington Disease; Krabbe Disease (Infantile); Mitochondrial DNA-Associated Leigh Syndrome and NARP; Lesch-Nyhan Syndrome; LIS1-Associated Lissencephaly; Lowe Syndrome; Maple Syrup Urine Disease; MECP2 Duplication Syndrome; ATP7A-Related Copper Transport Disorders; LAMA2-Related Muscular Dystrophy; Arylsulfatase A Deficiency; Mucopolysaccharidosis Types I, II or III; Peroxisome Biogenesis Disorders, Zellweger Syndrome Spectrum; Neurodegeneration with Brain Iron Accumulation Disorders; Acid Sphingomyelinase Deficiency; Niemann-Pick Disease Type C; Glycine Encephalopathy; ARX-Related Disorders; Urea Cycle Disorders; COL1A1/2-Related Osteogenesis Imperfecta; Mitochondrial DNA Deletion Syndromes; PLP1-Related Disorders; Perry Syndrome; Phelan-McDermid Syndrome; Glycogen Storage Disease Type II (Pompe Disease) (Infantile); MAPT-Related Disorders; MECP2-Related Disorders; Rhizomelic Chondrodysplasia Punctata Type 1; Roberts Syndrome; Sandhoff Disease; Schindler Disease-Type 1; Adenosine Deaminase Deficiency; Smith-Lemli-Opitz Syndrome; Spinal Muscular Atrophy; Infantile-Onset Spinocerebellar Ataxia; Hexosaminidase A Deficiency; Thanatophoric Dysplasia Type 1; Collagen Type VI-Related Disorders; Usher Syndrome Type I; Congenital Muscular Dystrophy; Wolf-Hirschhorn Syndrome; Lysosomal Acid Lipase Deficiency; and Xeroderma Pigmentosum.

As will be apparent, it is envisaged that the present system can be used to target any polynucleotide sequence of interest. Some examples of conditions or diseases that might be usefully treated using the present system are included in the Tables above and examples of genes currently associated with those conditions are also provided there. However, the genes exemplified are not exhaustive.

EXAMPLES

The following examples are given for the purpose of illustrating various embodiments of the invention and are not meant to limit the present invention in any fashion. The present examples, along with the methods described herein are presently representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the invention. Changes therein and other uses which are encompassed within the spirit of the invention as defined by the scope of the claims will occur to those skilled in the art.

Example 1: CRISPR Complex Activity in the Nucleus of a Eukaryotic Cell

An example type II CRISPR system is the type II CRISPR locus from Streptococcus pyogenes SF370, which contains a cluster of four genes Cas9, Cas1, Cas2, and Csn1, as well as two non-coding RNA elements, tracrRNA and a characteristic array of repetitive sequences (direct repeats) interspaced by short stretches of non-repetitive sequences (spacers, about 30 bp each). In this system, targeted DNA double-strand break (DSB) is generated in four sequential steps (FIG. 2A). First, two non-coding RNAs, the pre-crRNA array and tracrRNA, are transcribed from the CRISPR locus. Second, tracrRNA hybridizes to the direct repeats of pre-crRNA, which is then processed into mature crRNAs containing individual spacer sequences. Third, the mature crRNA:tracrRNA complex directs Cas9 to the DNA target consisting of the protospacer and the corresponding PAM via heteroduplex formation between the spacer region of the crRNA and the protospacer DNA. Finally, Cas9 mediates cleavage of target DNA upstream of PAM to create a DSB within the protospacer (FIG. 2A). This example describes an example process for adapting this RNA-programmable nuclease system to direct CRISPR complex activity in the nuclei of eukaryotic cells.

Cell Culture and Transfection

Human embryonic kidney (HEK) cell line HEK 293FT (Life Technologies) was maintained in Dulbecco's modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (HyClone), 2 mM GlutaMAX (Life Technologies), 100 U/mL penicillin, and 100 μg/mL streptomycin at 37° C. with 5% CO₂ incubation. Mouse neuro2A (N2A) cell line (ATCC) was maintained with DMEM supplemented with 5% fetal bovine serum (HyClone), 2 mM GlutaMAX (Life Technologies), 100U/mL penicillin, and 100 μg/mL streptomycin at 37° C. with 5% CO₂.

HEK 293FT or N2A cells were seeded into 24-well plates (Corning) one day prior to transfection at a density of 200,000 cells per well. Cells were transfected using Lipofectamine 2000 (Life Technologies) following the manufacturer's recommended protocol. For each well of a 24-well plate a total of 800 ng of plasmids were used.

Surveyor Assay and Sequencing Analysis for Genome Modification

HEK 293FT or N2A cells were transfected with plasmid DNA as described above. After transfection, the cells were incubated at 37° C. for 72 hours before genomic DNA extraction. Genomic DNA was extracted using the QuickExtract DNA extraction kit (Epicentre) following the manufacturer's protocol. Briefly, cells were resuspended in QuickExtract solution and incubated at 65° C. for 15 minutes and 98° C. for 10 minutes. Extracted genomic DNA was immediately processed or stored at −20° C.

The genomic region surrounding a CRISPR target site for each gene was PCR amplified, and products were purified using QiaQuick Spin Column (Qiagen) following manufacturer's protocol. A total of 400 ng of the purified PCR products were mixed with 2 μl 10×Taq polymerase PCR buffer (Enzymatics) and ultrapure water to a final volume of 200, and subjected to a re-annealing process to enable heteroduplex formation: 95° C. for 10 min, 95° C. to 85° C. ramping at −2° C./s, 85° C. to 25° C. at −0.25° C./s, and 25° C. hold for 1 minute. After re-annealing, products were treated with Surveyor nuclease and Surveyor enhancer S (Transgenomics) following the manufacturer's recommended protocol, and analyzed on 4-20% Novex TBE poly-acrylamide gels (Life Technologies). Gels were stained with SYBR Gold DNA stain (Life Technologies) for 30 minutes and imaged with a Gel Doc gel imaging system (Bio-rad). Quantification was based on relative band intensities, as a measure of the fraction of cleaved DNA. FIG. 7 provides a schematic illustration of this Surveyor assay.

Restriction Fragment Length Polymorphism Assay for Detection of Homologous Recombination.

HEK 293FT and N2A cells were transfected with plasmid DNA, and incubated at 37° C. for 72 hours before genomic DNA extraction as described above. The target genomic region was PCR amplified using primers outside the homology arms of the homologous recombination (HR) template. PCR products were separated on a 1% agarose gel and extracted with MinElute GelExtraction Kit (Qiagen). Purified products were digested with HindIII (Fermentas) and analyzed on a 6% Novex TBE poly-acrylamide gel (Life Technologies).

RNA Secondary Structure Prediction and Analysis

RNA secondary structure prediction was performed using the online webserver RNAfold developed at Institute for Theoretical Chemistry at the University of Vienna, using the centroid structure prediction algorithm (see e.g. A. R. Gruber et al., 2008, Cell 106(1): 23-24; and P A Carr and G M Church, 2009, Nature Biotechnology 27(12): 1151-62).

RNA Purification

HEK 293FT cells were maintained and transfected as stated above. Cells were harvested by trypsinization followed by washing in phosphate buffered saline (PBS). Total cell RNA was extracted with TRI reagent (Sigma) following manufacturer's protocol. Extracted total RNA was quantified using Naonodrop (Thermo Scientific) and normalized to same concentration.

Northern Blot Analysis of crRNA and tracrRNA Expression in Mammalian Cells

RNAs were mixed with equal volumes of 2× loading buffer (Ambion), heated to 95° C. for 5 min, chilled on ice for 1 min, and then loaded onto 8% denaturing polyacrylamide gels (SequaGel, National Diagnostics) after pre-running the gel for at least 30 minutes. The samples were electrophoresed for 1.5 hours at 40W limit. Afterwards, the RNA was transferred to Hybond N+ membrane (GE Healthcare) at 300 mA in a semi-dry transfer apparatus (Bio-rad) at room temperature for 1.5 hours. The RNA was crosslinked to the membrane using autocrosslink button on Stratagene UV Crosslinker the Stratalinker (Stratagene). The membrane was pre-hybridized in ULTRAhyb-Oligo Hybridization Buffer (Ambion) for 30 min with rotation at 42° C., and probes were then added and hybridized overnight. Probes were ordered from IDT and labeled with [gamma ³²P] ATP (Perkin Elmer) with T4 polynucleotide kinase (New England Biolabs). The membrane was washed once with pre-warmed (42° C.) 2×SSC, 0.5% SDS for 1 min followed by two 30 minute washes at 42° C. The membrane was exposed to a phosphor screen for one hour or overnight at room temperature and then scanned with a phosphorimager (Typhoon).

Bacterial CRISPR System Construction and Evaluation

CRISPR locus elements, including tracrRNA, Cas9, and leader were PCR amplified from Streptococcus pyogenes SF370 genomic DNA with flanking homology arms for Gibson Assembly. Two BsaI type IIS sites were introduced in between two direct repeats to facilitate easy insertion of spacers (FIG. 8). PCR products were cloned into EcoRV-digested pACYC184 downstream of the tet promoter using Gibson Assembly Master Mix (NEB). Other endogenous CRISPR system elements were omitted, with the exception of the last 50 bp of Csn2. Oligos (Integrated DNA Technology) encoding spacers with complimentary overhangs were cloned into the BsaI-digested vector pDC000 (NEB) and then ligated with T7 ligase (Enzymatics) to generate pCRISPR plasmids. Challenge plasmids containing spacers with PAM expression in mammalian cells (expression constructs illustrated in FIG. 6A, with functionality as determined by results of the Surveyor assay shown in FIG. 6B). Transcription start sites are marked as +1, and transcription terminator and the sequence probed by northern blot are also indicated. Expression of processed tracrRNA was also confirmed by Northern blot. FIG. 6C shows results of a Northern blot analysis of total RNA extracted from 293FT cells transfected with U6 expression constructs carrying long or short tracrRNA, as well as SpCas9 and DR-EMX1(1)-DR. Left and right panels are from 293FT cells transfected without or with SpRNase III, respectively. U6 indicate loading control blotted with a probe targeting human U6 snRNA. Transfection of the short tracrRNA expression construct led to abundant levels of the processed form of tracrRNA (˜75 bp). Very low amounts of long tracrRNA are detected on the Northern blot.

To promote precise transcriptional initiation, the RNA polymerase III-based U6 promoter was selected to drive the expression of tracrRNA (FIG. 2C). Similarly, a U6 promoter-based construct was developed to express a pre-crRNA array consisting of a single spacer flanked by two direct repeats (DRs, also encompassed by the term “tracr-mate sequences”; FIG. 2C). The initial spacer was designed to target a 33-base-pair (bp) target site (30-bp protospacer plus a 3-bp CRISPR motif (PAM) sequence satisfying the NGG recognition motif of Cas9) in the human EMXJ locus (FIG. 2C), a key gene in the development of the cerebral cortex.

To test whether heterologous expression of the CRISPR system (SpCas9, SpRNase III, tracrRNA, and pre-crRNA) in mammalian cells can achieve targeted cleavage of mammalian chromosomes, HEK 293FT cells were transfected with combinations of CRISPR components. Since DSBs in mammalian nuclei are partially repaired by the non-homologous end joining (NHEJ) pathway, which leads to the formation of indels, the Surveyor assay was used to detect potential cleavage activity at the target EMXJ locus (FIG. 7) (see e.g. Guschin et al., 2010, Methods Mol Biol 649: 247). Co-transfection of all four CRISPR components was able to induce up to 5.0% cleavage in the protospacer (see FIG. 2D). Co-transfection of all CRISPR components minus SpRNase III also induced up to 4.7% indel in the protospacer, suggesting that there may be endogenous mammalian RNases that are capable of assisting with crRNA maturation, such as for example the related Dicer and Drosha enzymes. Removing any of the remaining three components abolished the genome cleavage activity of the CRISPR system (FIG. 2D). Sanger sequencing of amplicons containing the target locus verified the cleavage activity: in 43 sequenced clones, 5 mutated alleles (11.6%) were found. Similar experiments using a variety of guide sequences produced indel percentages as high as 29% (see FIGS. 3-6, 10, and 11). These results define a three-component system for efficient CRISPR-mediated genome modification in mammalian cells. To optimize the cleavage efficiency, Applicants also tested whether different isoforms of tracrRNA affected the cleavage efficiency and found that, in this example system, only the short (89-bp) transcript form was able to mediate cleavage of the human EMX1 genomic locus (FIG. 6B).

FIG. 12 provides an additional Northern blot analysis of crRNA processing in mammalian cells. FIG. 12A illustrates a schematic showing the expression vector for a single spacer flanked by two direct repeats (DR-EMX1(1)-DR). The 30 bp spacer targeting the human EMX1 locus protospacer 1 (see FIG. 6) and the direct repeat sequences are shown in the sequence beneath FIG. 12A. The line indicates the region whose reverse-complement sequence was used to generate Northern blot probes for EMX1(1) crRNA detection. FIG. 12B shows a Northern blot analysis of total RNA extracted from 293FT cells transfected with U6 expression constructs carrying DR-EMX1(1)-DR. Left and right panels are from 293FT cells transfected without or with SpRNase III respectively. DR-EMX1(1)-DR was processed into mature crRNAs only in the presence of SpCas9 and short tracrRNA and was not dependent on the presence of SpRNase III. The mature crRNA detected from transfected 293FT total RNA is ˜33 bp and is shorter than the 39-42 bp mature crRNA from S. pyogenes. These results demonstrate that a CRISPR system can be transplanted into eukaryotic cells and reprogrammed to facilitate cleavage of endogenous mammalian target polynucleotides.

FIG. 2 illustrates the bacterial CRISPR system described in this example. FIG. 2A illustrates a schematic showing the CRISPR locus 1 from Streptococcus pyogenes SF370 and a proposed mechanism of CRISPR-mediated DNA cleavage by this system. Mature crRNA processed from the direct repeat-spacer array directs Cas9 to genomic targets consisting of complimentary protospacers and a protospacer-adjacent motif (PAM). Upon target-spacer base pairing, Cas9 mediates a double-strand break in the target DNA. FIG. 2B illustrates engineering of S. pyogenes Cas9 (SpCas9) and RNase III (SpRNase III) with nuclear localization signals (NLSs) to enable import into the mammalian nucleus. FIG. 2C illustrates mammalian expression of SpCas9 and SpRNase III driven by the constitutive EF1a promoter and tracrRNA and pre-crRNA array (DR-Spacer-DR) driven by the RNA Pol3 promoter U6 to promote precise transcription initiation and termination. A protospacer from the human EMX1 locus with a satisfactory PAM sequence is used as the spacer in the pre-crRNA array. FIG. 2D illustrates surveyor nuclease assay for SpCas9-mediated minor insertions and deletions. SpCas9 was expressed with and without SpRNase III, tracrRNA, and a pre-crRNA array carrying the EMX1-target spacer. FIG. 2E illustrates a schematic representation of base pairing between target locus and EMX1-targeting crRNA, as well as an example chromatogram showing a micro deletion adjacent to the SpCas9 cleavage site. FIG. 2F illustrates mutated alleles identified from sequencing analysis of 43 clonal amplicons showing a variety of micro insertions and deletions. Dashes indicate deleted bases, and non-aligned or mismatched bases indicate insertions or mutations. Scale bar=10 μm.

To further simplify the three-component system, a chimeric crRNA-tracrRNA hybrid design was adapted, where a mature crRNA (comprising a guide sequence) may be fused to a partial tracrRNA via a stem-loop to mimic the natural crRNA:tracrRNA duplex. To increase co-delivery efficiency, a bicistronic expression vector was created to drive co-expression of a chimeric RNA and SpCas9 in transfected cells. In parallel, the bicistronic vectors were used to express a pre-crRNA (DR-guide sequence-DR) with SpCas9, to induce processing into crRNA with a separately expressed tracrRNA (compare FIG. 11B top and bottom). FIG. 8 provides schematic illustrations of bicistronic expression vectors for pre-crRNA array (FIG. 8A) or chimeric crRNA (represented by the short line downstream of the guide sequence insertion site and upstream of the EF1a promoter in FIG. 8B) with hSpCas9, showing location of various elements and the point of guide sequence insertion. The expanded sequence around the location of the guide sequence insertion site in FIG. 8B also shows a partial DR sequence (GTTTTAGAGCTA) (SEQ ID NO: 11) and a partial tracrRNA sequence (TAGCAAGTTAAAATAAGGCTAGTCCGTTTTT)(SEQ ID NO: 12). Guide sequences can be inserted between BbsI sites using annealed oligonucleotides. Sequence designs for the oligonucleotides are shown below the schematic illustrations in FIG. 8, with appropriate ligation adapters indicated. WPRE represents the Woodchuck hepatitis virus post-transcriptional regulatory element. The efficiency of chimeric RNA-mediated cleavage was tested by targeting the same EMX1 locus described above. Using both Surveyor assay and Sanger sequencing of amplicons, Applicants confirmed that the chimeric RNA design facilitates cleavage of human EMX1 locus with approximately a 4.7% modification rate (FIG. 3).

Generalizability of CRISPR-mediated cleavage in eukaryotic cells was tested by targeting additional genomic loci in both human and mouse cells by designing chimeric RNA targeting multiple sites in the human EMX1 and PVALB, as well as the mouse Th loci. FIG. 13 illustrates the selection of some additional targeted protospacers in human PVALB (FIG. 13A) and mouse Th (FIG. 13B) loci. Schematics of the gene loci and the location of three protospacers within the last exon of each are provided. The underlined sequences include 30 bp of protospacer sequence and 3 bp at the 3′ end corresponding to the PAM sequences. Protospacers on the sense and anti-sense strands are indicated above and below the DNA sequences, respectively. A modification rate of 6.3% and 0.75% was achieved for the human PVALB and mouse Th loci respectively, demonstrating the broad applicability of the CRISPR system in modifying different loci across multiple organisms (FIG. 5). While cleavage was only detected with one out of three spacers for each locus using the chimeric constructs, all target sequences were cleaved with efficiency of indel production reaching 27% when using the co-expressed pre-crRNA arrangement (FIGS. 6 and 13).

FIG. 11 provides a further illustration that SpCas9 can be reprogrammed to target multiple genomic loci in mammalian cells. FIG. 11A provides a schematic of the human EMX1 locus showing the location of five protospacers, indicated by the underlined sequences. FIG. 11B provides a schematic of the pre-crRNA/trcrRNA complex showing hybridization between the direct repeat region of the pre-crRNA and tracrRNA (top), and a schematic of a chimeric RNA design comprising a 20 bp guide sequence, and tracr mate and tracr sequences consisting of partial direct repeat and tracrRNA sequences hybridized in a hairpin structure (bottom). Results of a Surveyor assay comparing the efficacy of Cas9-mediated cleavage at five protospacers in the human EMX1 locus is illustrated in FIG. 11C. Each protospacer is targeted using either processed pre-crRNA/tracrRNA complex (crRNA) or chimeric RNA (chiRNA).

Since the secondary structure of RNA can be crucial for intermolecular interactions, a structure prediction algorithm based on minimum free energy and Boltzmann-weighted structure ensemble was used to compare the putative secondary structure of all guide sequences used in the genome targeting experiment (see e.g. Gruber et al., 2008, Nucleic Acids Research, 36: W70). Analysis revealed that in most cases, the effective guide sequences in the chimeric crRNA context were substantially free of secondary structure motifs, whereas the ineffective guide sequences were more likely to form internal secondary structures that could prevent base pairing with the target protospacer DNA. It is thus possible that variability in the spacer secondary structure might impact the efficiency of CRISPR-mediated interference when using a chimeric crRNA.

Further vector designs for SpCas9 are shown in FIG. 22, which illustrates single expression vectors incorporating a U6 promoter linked to an insertion site for a guide oligo, and a Cbh promoter linked to SpCas9 coding sequence. The vector shown in FIG. 22b includes a tracrRNA coding sequence linked to an H1 promoter.

In the bacterial assay, all spacers facilitated efficient CRISPR interference (FIG. 3C). These results suggest that there may be additional factors affecting the efficiency of CRISPR activity in mammalian cells.

To investigate the specificity of CRISPR-mediated cleavage, the effect of single-nucleotide mutations in the guide sequence on protospacer cleavage in the mammalian genome was analyzed using a series of EMX1-targeting chimeric crRNAs with single point mutations (FIG. 3A). FIG. 3B illustrates results of a Surveyor nuclease assay comparing the cleavage efficiency of Cas9 when paired with different mutant chimeric RNAs. Single-base mismatch up to 12-bp 5′ of the PAM substantially abrogated genomic cleavage by SpCas9, whereas spacers with mutations at farther upstream positions retained activity against the original protospacer target (FIG. 3B). In addition to the PAM, SpCas9 has single-base specificity within the last 12-bp of the spacer. Furthermore, CRISPR is able to mediate genomic cleavage as efficiently as a pair of TALE nucleases (TALEN) targeting the same EMX1 protospacer. FIG. 3C provides a schematic showing the design of TALENs targeting EMX1, and FIG. 3D shows a Surveyor gel comparing the efficiency of TALEN and Cas9 (n=3).

Having established a set of components for achieving CRISPR-mediated gene editing in mammalian cells through the error-prone NHEJ mechanism, the ability of CRISPR to stimulate homologous recombination (HR), a high fidelity gene repair pathway for making precise edits in the genome, was tested. The wild type SpCas9 is able to mediate site-specific DSBs, which can be repaired through both NHEJ and HR. In addition, an aspartate-to-alanine substitution (D10A) in the RuvC I catalytic domain of SpCas9 was engineered to convert the nuclease into a nickase (SpCas9n; illustrated in FIG. 4A) (see e.g. Sapranausaks et al., 2011, Nucleic Acids Research, 39: 9275; Gasiunas et al., 2012, Proc. Natl. Acad. Sci. USA, 109:E2579), such that nicked genomic DNA undergoes the high-fidelity homology-directed repair (HDR). Surveyor assay confirmed that SpCas9n does not generate indels at the EMX1 protospacer target. As illustrated in FIG. 4B, co-expression of EMXJ-targeting chimeric crRNA with SpCas9 produced indels in the target site, whereas co-expression with SpCas9n did not (n=3). Moreover, sequencing of 327 amplicons did not detect any indels induced by SpCas9n. The same locus was selected to test CRISPR-mediated HR by co-transfecting HEK 293FT cells with the chimeric RNA targeting EMX1, hSpCas9 or hSpCas9n, as well as a HR template to introduce a pair of restriction sites (HindIII and NheI) near the protospacer. FIG. 4C provides a schematic illustration of the HR strategy, with relative locations of recombination points and primer annealing sequences (arrows). SpCas9 and SpCas9n indeed catalyzed integration of the HR template into the EMX1 locus. PCR amplification of the target region followed by restriction digest with HindIII revealed cleavage products corresponding to expected fragment sizes (arrows in restriction fragment length polymorphism gel analysis shown in FIG. 4D), with SpCas9 and SpCas9n mediating similar levels of HR efficiencies. Applicants further verified HR using Sanger sequencing of genomic amplicons (FIG. 4E). These results demonstrate the utility of CRISPR for facilitating targeted gene insertion in the mammalian genome. Given the 14-bp (12-bp from the spacer and 2-bp from the PAM) target specificity of the wild type SpCas9, the availability of a nickase can significantly reduce the likelihood of off-target modifications, since single strand breaks are not substrates for the error-prone NHEJ pathway.

Expression constructs mimicking the natural architecture of CRISPR loci with arrayed spacers (FIG. 2A) were constructed to test the possibility of multiplexed sequence targeting. Using a single CRISPR array encoding a pair of EMX1- and PVALB-targeting spacers, efficient cleavage at both loci was detected (FIG. 4F, showing both a schematic design of the crRNA array and a Surveyor blot showing efficient mediation of cleavage). Targeted deletion of larger genomic regions through concurrent DSBs using spacers against two targets within EMX1 spaced by 119 bp was also tested, and a 1.6% deletion efficacy (3 out of 182 amplicons; FIG. 4G) was detected. This demonstrates that the CRISPR system can mediate multiplexed editing within a single genome.

Example 2: CRISPR System Modifications and Alternatives

The ability to use RNA to program sequence-specific DNA cleavage defines a new class of genome engineering tools for a variety of research and industrial applications. Several aspects of the CRISPR system can be further improved to increase the efficiency and versatility of CRISPR targeting. Optimal Cas9 activity may depend on the availability of free Mg²⁺ at levels higher than that present in the mammalian nucleus (see e.g. Jinek et al., 2012, Science, 337:816), and the preference for an NGG motif immediately downstream of the protospacer restricts the ability to target on average every 12-bp in the human genome (FIG. 9, evaluating both plus and minus strands of human chromosomal sequences). Some of these constraints can be overcome by exploring the diversity of CRISPR loci across the microbial metagenome (see e.g. Makarova et al., 2011, Nat Rev Microbiol, 9:467). Other CRISPR loci may be transplanted into the mammalian cellular milieu by a process similar to that described in Example 1. For example, FIG. 10 illustrates adaptation of the Type II CRISPR system from CRISPR 1 of Streptococcus thermophilus LMD-9 for heterologous expression in mammalian cells to achieve CRISPR-mediated genome editing. FIG. 10A provides a Schematic illustration of CRISPR 1 from S. thermophilus LMD-9. FIG. 10B illustrates the design of an expression system for the S. thermophilus CRISPR system. Human codon-optimized hStCas9 is expressed using a constitutive EF1α promoter. Mature versions of tracrRNA and crRNA are expressed using the U6 promoter to promote precise transcription initiation. Sequences from the mature crRNA and tracrRNA are illustrated. A single base indicated by the lower case “a” in the crRNA sequence is used to remove the polyU sequence, which serves as a RNA polIII transcriptional terminator. FIG. 10C provides a schematic showing guide sequences targeting the human EMX1 locus. FIG. 10D shows the results of hStCas9-mediated cleavage in the target locus using the Surveyor assay. RNA guide spacers 1 and 2 induced 14% and 6.4%, respectively. Statistical analysis of cleavage activity across biological replica at these two protospacer sites is also provided in FIG. 5. FIG. 14 provides a schematic of additional protospacer and corresponding PAM sequence targets of the S. thermophilus CRISPR system in the human EMX1 locus. Two protospacer sequences are highlighted and their corresponding PAM sequences satisfying NNAGAAW motif are indicated by underlining 3′ with respect to the corresponding highlighted sequence. Both protospacers target the anti-sense strand.

Example 3: Sample Target Sequence Selection Algorithm

A software program is designed to identify candidate CRISPR target sequences on both strands of an input DNA sequence based on desired guide sequence length and a CRISPR motif sequence (PAM) for a specified CRISPR enzyme. For example, target sites for Cas9 from S. pyogenes, with PAM sequences NGG, may be identified by searching for 5′-N_(x)-NGG-3′ both on the input sequence and on the reverse-complement of the input. Likewise, target sites for Cas9 of S. thermophilus CRISPR1, with PAM sequence NNAGAAW, may be identified by searching for 5′-N_(x)-NNAGAAW-3′ (SEQ ID NO: 13) both on the input sequence and on the reverse-complement of the input. Likewise, target sites for Cas9 of S. thermophilus CRISPR3, with PAM sequence NGGNG, may be identified by searching for 5′-N_(x)-NGGNG-3′ both on the input sequence and on the reverse-complement of the input. The value “x” in N_(x) may be fixed by the program or specified by the user, such as 20.

Since multiple occurrences in the genome of the DNA target site may lead to nonspecific genome editing, after identifying all potential sites, the program filters out sequences based on the number of times they appear in the relevant reference genome. For those CRISPR enzymes for which sequence specificity is determined by a ‘seed’ sequence, such as the 11-12 bp 5′ from the PAM sequence, including the PAM sequence itself, the filtering step may be based on the seed sequence. Thus, to avoid editing at additional genomic loci, results are filtered based on the number of occurrences of the seed:PAM sequence in the relevant genome. The user may be allowed to choose the length of the seed sequence. The user may also be allowed to specify the number of occurrences of the seed:PAM sequence in a genome for purposes of passing the filter. The default is to screen for unique sequences. Filtration level is altered by changing both the length of the seed sequence and the number of occurrences of the sequence in the genome. The program may in addition or alternatively provide the sequence of a guide sequence complementary to the reported target sequence(s) by providing the reverse complement of the identified target sequence(s). An example visualization of some target sites in the human genome is provided in FIG. 18.

Further details of methods and algorithms to optimize sequence selection can be found in U.S. application Ser. No. 61/064,798 (Attorney docket 44790.11.2022; Broad Reference BI-2012/084); incorporated herein by reference.

Example 4: Evaluation of Multiple Chimeric crRNA-tracrRNA Hybrids

This example describes results obtained for chimeric RNAs (chiRNAs; comprising a guide sequence, a tracr mate sequence, and a tracr sequence in a single transcript) having tracr sequences that incorporate different lengths of wild-type tracrRNA sequence. FIG. 16a illustrates a schematic of a bicistronic expression vector for chimeric RNA and Cas9. Cas9 is driven by the CBh promoter and the chimeric RNA is driven by a U6 promoter. The chimeric guide RNA consists of a 20 bp guide sequence (Ns) joined to the tracr sequence (running from the first “U” of the lower strand to the end of the transcript), which is truncated at various positions as indicated. The guide and tracr sequences are separated by the tracr-mate sequence GUUUUAGAGCUA (SEQ ID NO: 14) followed by the loop sequence GAAA. Results of SURVEYOR assays for Cas9-mediated indels at the human EMX1 and PVALB loci are illustrated in FIGS. 16b and 16c , respectively. Arrows indicate the expected SURVEYOR fragments. ChiRNAs are indicated by their “+n” designation, and crRNA refers to a hybrid RNA where guide and tracr sequences are expressed as separate transcripts. Quantification of these results, performed in triplicate, are illustrated by histogram in FIGS. 17a and 17b , corresponding to FIGS. 16b and 16c , respectively (“N.D.” indicates no indels detected). Protospacer IDs and their corresponding genomic target, protospacer sequence, PAM sequence, and strand location are provided in Table D. Guide sequences were designed to be complementary to the entire protospacer sequence in the case of separate transcripts in the hybrid system, or only to the underlined portion in the case of chimeric RNAs.

TABLE D (SEQ ID NOs: 15-19, respectively, in order of appearance) protospacer genomic ID target protospacer sequence (5′ to 3′) PAM strand 1 EMX1 GGACATCGATGTCACCTCCAATGACTAGGG TGG + 2 EMX1 CATTGGAGGTGACATCGATGTCCTCCCCAT TGG - 3 EMX1 GGAAGGGCCTGAGTCCGAGCAGAAGAAGAA GGG + 4 PVALB GGTGGCGAGAGGGGCCGAGATTGGGTGTTC AGG + 5 PVALB ATGCAGGAGGGTGGCGAGAGGGGCCGAGAT TGG +

Further details to optimize guide sequences can be found in U.S. application Ser. No. 61/836,127 (Attorney docket 44790.08.2022; Broad Reference BI-2013/004G); incorporated herein by reference.

Initially, three sites within the EMX1 locus in human HEK 293FT cells were targeted. Genome modification efficiency of each chiRNA was assessed using the SURVEYOR nuclease assay, which detects mutations resulting from DNA double-strand breaks (DSBs) and their subsequent repair by the non-homologous end joining (NHEJ) DNA damage repair pathway. Constructs designated chiRNA(+n) indicate that up to the +n nucleotide of wild-type tracrRNA is included in the chimeric RNA construct, with values of 48, 54, 67, and 85 used for n. Chimeric RNAs containing longer fragments of wild-type tracrRNA (chiRNA(+67) and chiRNA(+85)) mediated DNA cleavage at all three EMX1 target sites, with chiRNA(+85) in particular demonstrating significantly higher levels of DNA cleavage than the corresponding crRNA/tracrRNA hybrids that expressed guide and tracr sequences in separate transcripts (FIGS. 16b and 17a ). Two sites in the PVALB locus that yielded no detectable cleavage using the hybrid system (guide sequence and tracr sequence expressed as separate transcripts) were also targeted using chiRNAs. chiRNA(+67) and chiRNA(+85) were able to mediate significant cleavage at the two PVALB protospacers (FIGS. 16c and 17b ).

For all five targets in the EMX1 and PVALB loci, a consistent increase in genome modification efficiency with increasing tracr sequence length was observed. Without wishing to be bound by any theory, the secondary structure formed by the 3′ end of the tracrRNA may play a role in enhancing the rate of CRISPR complex formation.

Example 5: Cas9 Diversity

The CRISPR-Cas system is an adaptive immune mechanism against invading exogenous DNA employed by diverse species across bacteria and archaea. The type II CRISPR-Cas9 system consists of a set of genes encoding proteins responsible for the “acquisition” of foreign DNA into the CRISPR locus, as well as a set of genes encoding the “execution” of the DNA cleavage mechanism; these include the DNA nuclease (Cas9), a non-coding transactivating cr-RNA (tracrRNA), and an array of foreign DNA-derived spacers flanked by direct repeats (crRNAs). Upon maturation by Cas9, the tracRNA and crRNA duplex guide the Cas9 nuclease to a target DNA sequence specified by the spacer guide sequences, and mediates double-stranded breaks in the DNA near a short sequence motif in the target DNA that is required for cleavage and specific to each CRISPR-Cas system. The type II CRISPR-Cas systems are found throughout the bacterial kingdom and highly diverse in in Cas9 protein sequence and size, tracrRNA and crRNA direct repeat sequence, genome organization of these elements, and the motif requirement for target cleavage. One species may have multiple distinct CRISPR-Cas systems.

Applicants evaluated 207 putative Cas9s from bacterial species identified based on sequence homology to known Cas9s and structures orthologous to known subdomains, including the HNH endonuclease domain and the RuvC endonuclease domains [information from the Eugene Koonin and Kira Makarova]. Phylogenetic analysis based on the protein sequence conservation of this set revealed five families of Cas9s, including three groups of large Cas9s (˜1400 amino acids) and two of small Cas9s (˜1100 amino acids) (see FIGS. 19 and 20A-F). Further details of Cas9s and mutations of the Cas9 enzyme to convert into a nickase or DNA binding protein and use of same with altered functionality can be found in U.S. application Serial Nos 61/836,101 and 61/835,936 (Attorney docket 44790.09.2022 and 4790.07.2022 and Broad Reference BI-2013/004E and BI-2013/004F respectively) incorporated herein by reference.

Example 6: Cas9 Orthologs

Applicants analyzed Cas9 orthologs to identify the relevant PAM sequences and the corresponding chimeric guide RNA. Having an expanded set of PAMs provides broader targeting across the genome and also significantly increases the number of unique target sites and provides potential for identifying novel Cas9s with increased levels of specificity in the genome.

The specificity of Cas9 orthologs can be evaluated by testing the ability of each Cas9 to tolerate mismatches between the guide RNA and its DNA target. For example, the specificity of SpCas9 has been characterized by testing the effect of mutations in the guide RNA on cleavage efficiency. Libraries of guide RNAs were made with single or multiple mismatches between the guide sequence and the target DNA. Based on these findings, target sites for SpCas9 can be selected based on the following guidelines:

To maximize SpCas9 specificity for editing a particular gene, one should choose a target site within the locus of interest such that potential ‘off-target’ genomic sequences abide by the following four constraints: First and foremost, they should not be followed by a PAM with either 5′-NGG or NAG sequences. Second, their global sequence similarity to the target sequence should be minimized. Third, a maximal number of mismatches should lie within the PAM-proximal region of the off-target site. Finally, a maximal number of mismatches should be consecutive or spaced less than four bases apart.

Similar methods can be used to evaluate the specificity of other Cas9 orthologs and to establish criteria for the selection of specific target sites within the genomes of target species. As mentioned previously phylogenetic analysis based on the protein sequence conservation of this set revealed five families of Cas9s, including three groups of large Cas9s (˜1400 amino acids) and two of small Cas9s (˜1100 amino acids) (see FIGS. 19 and 20A-F). Further details on Cas orthologs can be found in U.S. application Serial Nos 61/836,101 and 61/835,936 (Attorney docket 44790.09.2022 and 4790.07.2022 and Broad Reference BI-2013/004E and BI-2013/004F respectively) incorporated herein by reference.

Example 7: Engineering of Plants (Micro-Algae) Using Cas9 to Target and Manipulate Plant Genes

Methods of Delivering Cas9

Method 1: Applicants deliver Cas9 and guide RNA using a vector that expresses Cas9 under the control of a constitutive promoter such as Hsp70A-Rbc S2 or Beta2-tubulin. Method 2: Applicants deliver Cas9 and T7 polymerase using vectors that expresses Cas9 and T7 polymerase under the control of a constitutive promoter such as Hsp70A-Rbc S2 or Beta2-tubulin. Guide RNA will be delivered using a vector containing T7 promoter driving the guide RNA. Method 3: Applicants deliver Cas9 mRNA and in vitro transcribed guide RNA to algae cells. RNA can be in vitro transcribed. Cas9 mRNA will consist of the coding region for Cas9 as well as 3′UTR from Cop1 to ensure stabilization of the Cas9 mRNA. For Homologous recombination, Applicants provide an additional homology directed repair template.

Sequence for a cassette driving the expression of Cas9 under the control of beta-2 tubulin promoter, followed by the 3′ UTR of Cop1.

(SEQ ID NO: 20) TCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTA GGGCGGGCTGCGAGACGGCTTCCCGGCGCTGCATG CAACACCGATGATGCTTCGACCCCCCGAAGCTCCT TCGGGGCTGCATGGGCGCTCCGATGCCGCTCCAGG GCGAGCGCTGTTTAAATAGCCAGGCCCCCGATTGC AAAGACATTATAGCGAGCTACCAAAGCCATATTCA AACACCTAGATCACTACCACTTCTACACAGGCCAC TCGAGCTTGTGATCGCACTCCGCTAAGGGGGCGCC TCTTCCTCTTCGTTTCAGTCACAACCCGCAAACAT GTACCCATACGATGTTCCAGATTACGCTTCGCCGA AGAAAAAGCGCAAGGTCGAAGCGTCCGACAAGAAG TACAGCATCGGCCTGGACATCGGCACCAACTCTGT GGGCTGGGCCGTGATCACCGACGAGTACAAGGTGC CCAGCAAGAAATTCAAGGTGCTGGGCAACACCGAC CGGCACAGCATCAAGAAGAACCTGATCGGAGCCCT GCTGTTCGACAGCGGCGAAACAGCCGAGGCCACCC GGCTGAAGAGAACCGCCAGAAGAAGATACACCAGA CGGAAGAACCGGATCTGCTATCTGCAAGAGATCTT CAGCAACGAGATGGCCAAGGTGGACGACAGCTTCT TCCACAGACTGGAAGAGTCCTTCCTGGTGGAAGAG GATAAGAAGCACGAGCGGCACCCCATCTTCGGCAA CATCGTGGACGAGGTGGCCTACCACGAGAAGTACC CCACCATCTACCACCTGAGAAAGAAACTGGTGGAC AGCACCGACAAGGCCGACCTGCGGCTGATCTATCT GGCCCTGGCCCACATGATCAAGTTCCGGGGCCACT TCCTGATCGAGGGCGACCTGAACCCCGACAACAGC GACGTGGACAAGCTGTTCATCCAGCTGGTGCAGAC CTACAACCAGCTGTTCGAGGAAAACCCCATCAACG CCAGCGGCGTGGACGCCAAGGCCATCCTGTCTGCC AGACTGAGCAAGAGCAGACGGCTGGAAAATCTGAT CGCCCAGCTGCCCGGCGAGAAGAAGAATGGCCTGT TCGGCAACCTGATTGCCCTGAGCCTGGGCCTGACC CCCAACTTCAAGAGCAACTTCGACCTGGCCGAGGA TGCCAAACTGCAGCTGAGCAAGGACACCTACGACG ACGACCTGGACAACCTGCTGGCCCAGATCGGCGAC CAGTACGCCGACCTGTTTCTGGCCGCCAAGAACCT GTCCGACGCCATCCTGCTGAGCGACATCCTGAGAG TGAACACCGAGATCACCAAGGCCCCCCTGAGCGCC TCTATGATCAAGAGATACGACGAGCACCACCAGGA CCTGACCCTGCTGAAAGCTCTCGTGCGGCAGCAGC TGCCTGAGAAGTACAAAGAGATTTTCTTCGACCAG AGCAAGAACGGCTACGCCGGCTACATTGACGGCGG AGCCAGCCAGGAAGAGTTCTACAAGTTCATCAAGC CCATCCTGGAAAAGATGGACGGCACCGAGGAACTG CTCGTGAAGCTGAACAGAGAGGACCTGCTGCGGAA GCAGCGGACCTTCGACAACGGCAGCATCCCCCACC AGATCCACCTGGGAGAGCTGCACGCCATTCTGCGG CGGCAGGAAGATTTTTACCCATTCCTGAAGGACAA CCGGGAAAAGATCGAGAAGATCCTGACCTTCCGCA TCCCCTACTACGTGGGCCCTCTGGCCAGGGGAAAC AGCAGATTCGCCTGGATGACCAGAAAGAGCGAGGA AACCATCACCCCCTGGAACTTCGAGGAAGTGGTGG ACAAGGGCGCTTCCGCCCAGAGCTTCATCGAGCGG ATGACCAACTTCGATAAGAACCTGCCCAACGAGAA GGTGCTGCCCAAGCACAGCCTGCTGTACGAGTACT TCACCGTGTATAACGAGCTGACCAAAGTGAAATAC GTGACCGAGGGAATGAGAAAGCCCGCCTTCCTGAG CGGCGAGCAGAAAAAGGCCATCGTGGACCTGCTGT TCAAGACCAACCGGAAAGTGACCGTGAAGCAGCTG AAAGAGGACTACTTCAAGAAAATCGAGTGCTTCGA CTCCGTGGAAATCTCCGGCGTGGAAGATCGGTTCA ACGCCTCCCTGGGCACATACCACGATCTGCTGAAA ATTATCAAGGACAAGGACTTCCTGGACAATGAGGA AAACGAGGACATTCTGGAAGATATCGTGCTGACCC TGACACTGTTTGAGGACAGAGAGATGATCGAGGAA CGGCTGAAAACCTATGCCCACCTGTTCGACGACAA AGTGATGAAGCAGCTGAAGCGGCGGAGATACACCG GCTGGGGCAGGCTGAGCCGGAAGCTGATCAACGGC ATCCGGGACAAGCAGTCCGGCAAGACAATCCTGGA TTTCCTGAAGTCCGACGGCTTCGCCAACAGAAACT TCATGCAGCTGATCCACGACGACAGCCTGACCTTT AAAGAGGACATCCAGAAAGCCCAGGTGTCCGGCCA GGGCGATAGCCTGCACGAGCACATTGCCAATCTGG CCGGCAGCCCCGCCATTAAGAAGGGCATCCTGCAG ACAGTGAAGGTGGTGGACGAGCTCGTGAAAGTGAT GGGCCGGCACAAGCCCGAGAACATCGTGATCGAAA TGGCCAGAGAGAACCAGACCACCCAGAAGGGACAG AAGAACAGCCGCGAGAGAATGAAGCGGATCGAAGA GGGCATCAAAGAGCTGGGCAGCCAGATCCTGAAAG AACACCCCGTGGAAAACACCCAGCTGCAGAACGAG AAGCTGTACCTGTACTACCTGCAGAATGGGCGGGA TATGTACGTGGACCAGGAACTGGACATCAACCGGC TGTCCGACTACGATGTGGACCATATCGTGCCTCAG AGCTTTCTGAAGGACGACTCCATCGACAACAAGGT GCTGACCAGAAGCGACAAGAACCGGGGCAAGAGCG ACAACGTGCCCTCCGAAGAGGTCGTGAAGAAGATG AAGAACTACTGGCGGCAGCTGCTGAACGCCAAGCT GATTACCCAGAGAAAGTTCGACAATCTGACCAAGG CCGAGAGAGGCGGCCTGAGCGAACTGGATAAGGCC GGCTTCATCAAGAGACAGCTGGTGGAAACCCGGCA GATCACAAAGCACGTGGCACAGATCCTGGACTCCC GGATGAACACTAAGTACGACGAGAATGACAAGCTG ATCCGGGAAGTGAAAGTGATCACCCTGAAGTCCAA GCTGGTGTCCGATTTCCGGAAGGATTTCCAGTTTT ACAAAGTGCGCGAGATCAACAACTACCACCACGCC CACGACGCCTACCTGAACGCCGTCGTGGGAACCGC CCTGATCAAAAAGTACCCTAAGCTGGAAAGCGAGT TCGTGTACGGCGACTACAAGGTGTACGACGTGCGG AAGATGATCGCCAAGAGCGAGCAGGAAATCGGCAA GGCTACCGCCAAGTACTTCTTCTACAGCAACATCA TGAACTTTTTCAAGACCGAGATTACCCTGGCCAAC GGCGAGATCCGGAAGCGGCCTCTGATCGAGACAAA CGGCGAAACCGGGGAGATCGTGTGGGATAAGGGCC GGGATTTTGCCACCGTGCGGAAAGTGCTGAGCATG CCCCAAGTGAATATCGTGAAAAAGACCGAGGTGCA GACAGGCGGCTTCAGCAAAGAGTCTATCCTGCCCA AGAGGAACAGCGATAAGCTGATCGCCAGAAAGAAG GACTGGGACCCTAAGAAGTACGGCGGCTTCGACAG CCCCACCGTGGCCTATTCTGTGCTGGTGGTGGCCA AAGTGGAAAAGGGCAAGTCCAAGAAACTGAAGAGT GTGAAAGAGCTGCTGGGGATCACCATCATGGAAAG AAGCAGCTTCGAGAAGAATCCCATCGACTTTCTGG AAGCCAAGGGCTACAAAGAAGTGAAAAAGGACCTG ATCATCAAGCTGCCTAAGTACTCCCTGTTCGAGCT GGAAAACGGCCGGAAGAGAATGCTGGCCTCTGCCG GCGAACTGCAGAAGGGAAACGAACTGGCCCTGCCC TCCAAATATGTGAACTTCCTGTACCTGGCCAGCCA CTATGAGAAGCTGAAGGGCTCCCCCGAGGATAATG AGCAGAAACAGCTGTTTGTGGAACAGCACAAGCAC TACCTGGACGAGATCATCGAGCAGATCAGCGAGTT CTCCAAGAGAGTGATCCTGGCCGACGCTAATCTGG ACAAAGTGCTGTCCGCCTACAACAAGCACCGGGAT AAGCCCATCAGAGAGCAGGCCGAGAATATCATCCA CCTGTTTACCCTGACCAATCTGGGAGCCCCTGCCG CCTTCAAGTACTTTGACACCACCATCGACCGGAAG AGGTACACCAGCACCAAAGAGGTGCTGGACGCCAC CCTGATCCACCAGAGCATCACCGGCCTGTACGAGA CACGGATCGACCTGTCTCAGCTGGGAGGCGACAGC CCCAAGAAGAAGAGAAAGGTGGAGGCCAGCTAAGG ATCCGGCAAGACTGGCCCCGCTTGGCAACGCAACA GTGAGCCCCTCCCTAGTGTGTTTGGGGATGTGACT ATGTATTCGTGTGTTGGCCAACGGGTCAACCCGAA CAGATTGATACCCGCCTTGGCATTTCCTGTCAGAA TGTAACGTCAGTTGATGGTACT

Sequence for a cassette driving the expression of T7 polymerase under the control of beta-2 tubulin promoter, followed by the 3′ UTR of Copl:

(SEQ ID NO: 21) TCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTA GGGCGGGCTGCGAGACGGCTTCCCGGCGCTGCATG CAACACCGATGATGCTTCGACCCCCCGAAGCTCCT TCGGGGCTGCATGGGCGCTCCGATGCCGCTCCAGG GCGAGCGCTGTTTAAATAGCCAGGCCCCCGATTGC AAAGACATTATAGCGAGCTACCAAAGCCATATTCA AACACCTAGATCACTACCACTTCTACACAGGCCAC TCGAGCTTGTGATCGCACTCCGCTAAGGGGGCGCC TCTTCCTCTTCGTTTCAGTCACAACCCGCAAACat gcctaagaagaagaggaaggttaacacgattaaca tcgctaagaacgacttctctgacatcgaactggct gctatcccgttcaacactctggctgaccattacgg tgagcgtttagctcgcgaacagttggcccttgagc atgagtcttacgagatgggtgaagcacgcttccgc aagatgtttgagcgtcaacttaaagctggtgaggt tgcggataacgctgccgccaagcctctcatcacta ccctactccctaagatgattgcacgcatcaacgac tggtttgaggaagtgaaagctaagcgcggcaagcg cccgacagccttccagttcctgcaagaaatcaagc cggaagccgtagcgtacatcaccattaagaccact ctggcttgcctaaccagtgctgacaatacaaccgt tcaggctgtagcaagcgcaatcggtcgggccattg aggacgaggctcgcttcggtcgtatccgtgacctt gaagctaagcacttcaagaaaaacgttgaggaaca actcaacaagcgcgtagggcacgtctacaagaaag catttatgcaagttgtcgaggctgacatgctctct aagggtctactcggtggcgaggcgtggtcttcgtg gcataaggaagactctattcatgtaggagtacgct gcatcgagatgctcattgagtcaaccggaatggtt agcttacaccgccaaaatgctggcgtagtaggtca agactctgagactatcgaactcgcacctgaatacg ctgaggctatcgcaacccgtgcaggtgcgctggct ggcatctctccgatgttccaaccttgcgtagttcc tcctaagccgtggactggcattactggtggtggct attgggctaacggtcgtcgtcctctggcgctggtg cgtactcacagtaagaaagcactgatgcgctacga agacgtttacatgcctgaggtgtacaaagcgatta acattgcgcaaaacaccgcatggaaaatcaacaag aaagtcctagcggtcgccaacgtaatcaccaagtg gaagcattgtccggtcgaggacatccctgcgattg agcgtgaagaactcccgatgaaaccggaagacatc gacatgaatcctgaggctctcaccgcgtggaaacg tgctgccgctgctgtgtaccgcaaggacaaggctc gcaagtctcgccgtatcagccttgagttcatgctt gagcaagccaataagtttgctaaccataaggccat ctggttcccttacaacatggactggcgcggtcgtg tttacgctgtgtcaatgttcaacccgcaaggtaac gatatgaccaaaggactgcttacgctggcgaaagg taaaccaatcggtaaggaaggttactactggctga aaatccacggtgcaaactgtgcgggtgtcgacaag gttccgttccctgagcgcatcaagttcattgagga aaaccacgagaacatcatggcttgcgctaagtctc cactggagaacacttggtgggctgagcaagattct ccgttctgcttccttgcgttctgctttgagtacgc tggggtacagcaccacggcctgagctataactgct cccttccgctggcgtttgacgggtcttgctctggc atccagcacttctccgcgatgctccgagatgaggt aggtggtcgcgcggttaacttgcttcctagtgaaa ccgttcaggacatctacgggattgttgctaagaaa gtcaacgagattctacaagcagacgcaatcaatgg gaccgataacgaagtagttaccgtgaccgatgaga acactggtgaaatctctgagaaagtcaagctgggc actaaggcactggctggtcaatggctggcttacgg tgttactcgcagtgtgactaagcgttcagtcatga cgctggcttacgggtccaaagagttcggcttccgt caacaagtgctggaagataccattcagccagctat tgattccggcaagggtctgatgttcactcagccga atcaggctgctggatacatggctaagctgatttgg gaatctgtgagcgtgacggtggtagctgcggttga agcaatgaactggcttaagtctgctgctaagctgc tggctgctgaggtcaaagataagaagactggagag attcttcgcaagcgttgcgctgtgcattgggtaac tcctgatggtttccctgtgtggcaggaatacaaga agcctattcagacgcgcttgaacctgatgttcctc ggtcagttccgcttacagcctaccattaacaccaa caaagatagcgagattgatgcacacaaacaggagt ctggtatcgctcctaactttgtacacagccaagac ggtagccaccttcgtaagactgtagtgtgggcaca cgagaagtacggaatcgaatcttttgcactgattc acgactccttcggtacgattccggctgacgctgcg aacctgttcaaagcagtgcgcgaaactatggttga cacatatgagtcttgtgatgtactggctgatttct acgaccagttcgctgaccagttgcacgagtctcaa ttggacaaaatgccagcacttccggctaaaggtaa cttgaacctccgtgacatcttagagtcggacttcg cgttcgcgtaaGGATCCGGCAAGACTGGCCCCGCT TGGCAACGCAACAGTGAGCCCCTCCCTAGTGTGTT TGGGGATGTGACTATGTATTCGTGTGTTGGCCAAC GGGTCAACCCGAACAGATTGATACCCGCCTTGGCA TTTCCTGTCAGAATGTAACGTCAGTTGATGGTACT

Sequence of guide RNA driven by the T7 promoter (T7 promoter, Ns represent targeting sequence):

(SEQ ID NO: 22) gaaatTAATACGACTCACTATANNNNNNNNNNNNNNNNNNNNgttttaga gctaGAAAtagcaagttaaaataaggctagtccgttatcaacttgaaaaa gtggcaccgagtcggtgcttttttt

Gene Delivery:

Chlamydomonas reinhardtii strain CC-124 and CC-125 from the Chlamydomonas Resource Center will be used for electroporation. Electroporation protocol follows standard recommended protocol from the GeneArt Chlamydomonas Engineering kit.

Also, Applicants generate a line of Chlamydomonas reinhardtii that expresses Cas9 constitutively. This can be done by using pChlamy1 (linearized using PvuI) and selecting for hygromycin resistant colonies. Sequence for pChlamy1 containing Cas9 is below. In this way to achieve gene knockout one simply needs to deliver RNA for the guideRNA. For homologous recombination Applicants deliver guideRNA as well as a linearized homologous recombination template.

pChlamy1-Cas9: (SEQ ID NO: 23) TGCGGTATTTCACACCGCATCAGGTGGCACTTTTC GGGGAAATGTGCGCGGAACCCCTATTTGTTTATTT TTCTAAATACATTCAAATATGTATCCGCTCATGAG ATTATCAAAAAGGATCTTCACCTAGATCCTTTTAA ATTAAAAATGAAGTTTTAAATCAATCTAAAGTATA TATGAGTAAACTTGGTCTGACAGTTACCAATGCTT AATCAGTGAGGCACCTATCTCAGCGATCTGTCTAT TTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTG TAGATAACTACGATACGGGAGGGCTTACCATCTGG CCCCAGTGCTGCAATGATACCGCGAGACCCACGCT CACCGGCTCCAGATTTATCAGCAATAAACCAGCCA GCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAAC TTTATCCGCCTCCATCCAGTCTATTAATTGTTGCC GGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGT TTGCGCAACGTTGTTGCCATTGCTACAGGCATCGT GGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCA GCTCCGGTTCCCAACGATCAAGGCGAGTTACATGA TCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTT CGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCG CAGTGTTATCACTCATGGTTATGGCAGCACTGCAT AATTCTCTTACTGTCATGCCATCCGTAAGATGCTT TTCTGTGACTGGTGAGTACTCAACCAAGTCATTCT GAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGC CCGGCGTCAATACGGGATAATACCGCGCCACATAG CAGAACTTTAAAAGTGCTCATCATTGGAAAACGTT CTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTG TTGAGATCCAGTTCGATGTAACCCACTCGTGCACC CAACTGATCTTCAGCATCTTTTACTTTCACCAGCG TTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCC GCAAAAAAGGGAATAAGGGCGACACGGAAATGTTG AATACTCATACTCTTCCTTTTTCAATATTATTGAA GCATTTATCAGGGTTATTGTCTCATGACCAAAATC CCTTAACGTGAGTTTTCGTTCCACTGAGCGTCAGA CCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATC CTTTTTTTCTGCGCGTAATCTGCTGCTTGCAAACA AAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCC GGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAA CTGGCTTCAGCAGAGCGCAGATACCAAATACTGTT CTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAA GAACTCTGTAGCACCGCCTACATACCTCGCTCTGC TAATCCTGTTACCAGTGGCTGTTGCCAGTGGCGAT AAGTCGTGTCTTACCGGGTTGGACTCAAGACGATA GTTACCGGATAAGGCGCAGCGGTCGGGCTGAACGG GGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACG ACCTACACCGAACTGAGATACCTACAGCGTGAGCT ATGAGAAAGCGCCACGCTTCCCGAAGGGAGAAAGG CGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACA GGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGC CTGGTATCTTTATAGTCCTGTCGGGTTTCGCCACC TCTGACTTGAGCGTCGATTTTTGTGATGCTCGTCA GGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGC GGCCTTTTTACGGTTCCTGGCCTTTTGCTGGCCTT TTGCTCACATGTTCTTTCCTGCGTTATCCCCTGAT TCTGTGGATAACCGTATTACCGCCTTTGAGTGAGC TGATACCGCTCGCCGCAGCCGAACGACCGAGCGCA GCGAGTCAGTGAGCGAGGAAGCGGTCGCTGAGGCT TGACATGATTGGTGCGTATGTTTGTATGAAGCTAC AGGACTGATTTGGCGGGCTATGAGGGCGGGGGAAG CTCTGGAAGGGCCGCGATGGGGCGCGCGGCGTCCA GAAGGCGCCATACGGCCCGCTGGCGGCACCCATCC GGTATAAAAGCCCGCGACCCCGAACGGTGACCTCC ACTTTCAGCGACAAACGAGCACTTATACATACGCG ACTATTCTGCCGCTATACATAACCACTCAGCTAGC TTAAGATCCCATCAAGCTTGCATGCCGGGCGCGCC AGAAGGAGCGCAGCCAAACCAGGATGATGTTTGAT GGGGTATTTGAGCACTTGCAACCCTTATCCGGAAG CCCCCTGGCCCACAAAGGCTAGGCGCCAATGCAAG CAGTTCGCATGCAGCCCCTGGAGCGGTGCCCTCCT GATAAACCGGCCAGGGGGCCTATGTTCTTTACTTT TTTACAAGAGAAGTCACTCAACATCTTAAAATGGC CAGGTGAGTCGACGAGCAAGCCCGGCGGATCAGGC AGCGTGCTTGCAGATTTGACTTGCAACGCCCGCAT TGTGTCGACGAAGGCTTTTGGCTCCTCTGTCGCTG TCTCAAGCAGCATCTAACCCTGCGTCGCCGTTTCC ATTTGCAGGAGATTCGAGGTACCATGTACCCATAC GATGTTCCAGATTACGCTTCGCCGAAGAAAAAGCG CAAGGTCGAAGCGTCCGACAAGAAGTACAGCATCG GCCTGGACATCGGCACCAACTCTGTGGGCTGGGCC GTGATCACCGACGAGTACAAGGTGCCCAGCAAGAA ATTCAAGGTGCTGGGCAACACCGACCGGCACAGCA TCAAGAAGAACCTGATCGGAGCCCTGCTGTTCGAC AGCGGCGAAACAGCCGAGGCCACCCGGCTGAAGAG AACCGCCAGAAGAAGATACACCAGACGGAAGAACC GGATCTGCTATCTGCAAGAGATCTTCAGCAACGAG ATGGCCAAGGTGGACGACAGCTTCTTCCACAGACT GGAAGAGTCCTTCCTGGTGGAAGAGGATAAGAAGC ACGAGCGGCACCCCATCTTCGGCAACATCGTGGAC GAGGTGGCCTACCACGAGAAGTACCCCACCATCTA CCACCTGAGAAAGAAACTGGTGGACAGCACCGACA AGGCCGACCTGCGGCTGATCTATCTGGCCCTGGCC CACATGATCAAGTTCCGGGGCCACTTCCTGATCGA GGGCGACCTGAACCCCGACAACAGCGACGTGGACA AGCTGTTCATCCAGCTGGTGCAGACCTACAACCAG CTGTTCGAGGAAAACCCCATCAACGCCAGCGGCGT GGACGCCAAGGCCATCCTGTCTGCCAGACTGAGCA AGAGCAGACGGCTGGAAAATCTGATCGCCCAGCTG CCCGGCGAGAAGAAGAATGGCCTGTTCGGCAACCT GATTGCCCTGAGCCTGGGCCTGACCCCCAACTTCA AGAGCAACTTCGACCTGGCCGAGGATGCCAAACTG CAGCTGAGCAAGGACACCTACGACGACGACCTGGA CAACCTGCTGGCCCAGATCGGCGACCAGTACGCCG ACCTGTTTCTGGCCGCCAAGAACCTGTCCGACGCC ATCCTGCTGAGCGACATCCTGAGAGTGAACACCGA GATCACCAAGGCCCCCCTGAGCGCCTCTATGATCA AGAGATACGACGAGCACCACCAGGACCTGACCCTG CTGAAAGCTCTCGTGCGGCAGCAGCTGCCTGAGAA GTACAAAGAGATTTTCTTCGACCAGAGCAAGAACG GCTACGCCGGCTACATTGACGGCGGAGCCAGCCAG GAAGAGTTCTACAAGTTCATCAAGCCCATCCTGGA AAAGATGGACGGCACCGAGGAACTGCTCGTGAAGC TGAACAGAGAGGACCTGCTGCGGAAGCAGCGGACC TTCGACAACGGCAGCATCCCCCACCAGATCCACCT GGGAGAGCTGCACGCCATTCTGCGGCGGCAGGAAG ATTTTTACCCATTCCTGAAGGACAACCGGGAAAAG ATCGAGAAGATCCTGACCTTCCGCATCCCCTACTA CGTGGGCCCTCTGGCCAGGGGAAACAGCAGATTCG CCTGGATGACCAGAAAGAGCGAGGAAACCATCACC CCCTGGAACTTCGAGGAAGTGGTGGACAAGGGCGC TTCCGCCCAGAGCTTCATCGAGCGGATGACCAACT TCGATAAGAACCTGCCCAACGAGAAGGTGCTGCCC AAGCACAGCCTGCTGTACGAGTACTTCACCGTGTA TAACGAGCTGACCAAAGTGAAATACGTGACCGAGG GAATGAGAAAGCCCGCCTTCCTGAGCGGCGAGCAG AAAAAGGCCATCGTGGACCTGCTGTTCAAGACCAA CCGGAAAGTGACCGTGAAGCAGCTGAAAGAGGACT ACTTCAAGAAAATCGAGTGCTTCGACTCCGTGGAA ATCTCCGGCGTGGAAGATCGGTTCAACGCCTCCCT GGGCACATACCACGATCTGCTGAAAATTATCAAGG ACAAGGACTTCCTGGACAATGAGGAAAACGAGGAC ATTCTGGAAGATATCGTGCTGACCCTGACACTGTT TGAGGACAGAGAGATGATCGAGGAACGGCTGAAAA CCTATGCCCACCTGTTCGACGACAAAGTGATGAAG CAGCTGAAGCGGCGGAGATACACCGGCTGGGGCAG GCTGAGCCGGAAGCTGATCAACGGCATCCGGGACA AGCAGTCCGGCAAGACAATCCTGGATTTCCTGAAG TCCGACGGCTTCGCCAACAGAAACTTCATGCAGCT GATCCACGACGACAGCCTGACCTTTAAAGAGGACA TCCAGAAAGCCCAGGTGTCCGGCCAGGGCGATAGC CTGCACGAGCACATTGCCAATCTGGCCGGCAGCCC CGCCATTAAGAAGGGCATCCTGCAGACAGTGAAGG TGGTGGACGAGCTCGTGAAAGTGATGGGCCGGCAC AAGCCCGAGAACATCGTGATCGAAATGGCCAGAGA GAACCAGACCACCCAGAAGGGACAGAAGAACAGCC GCGAGAGAATGAAGCGGATCGAAGAGGGCATCAAA GAGCTGGGCAGCCAGATCCTGAAAGAACACCCCGT GGAAAACACCCAGCTGCAGAACGAGAAGCTGTACC TGTACTACCTGCAGAATGGGCGGGATATGTACGTG GACCAGGAACTGGACATCAACCGGCTGTCCGACTA CGATGTGGACCATATCGTGCCTCAGAGCTTTCTGA AGGACGACTCCATCGACAACAAGGTGCTGACCAGA AGCGACAAGAACCGGGGCAAGAGCGACAACGTGCC CTCCGAAGAGGTCGTGAAGAAGATGAAGAACTACT GGCGGCAGCTGCTGAACGCCAAGCTGATTACCCAG AGAAAGTTCGACAATCTGACCAAGGCCGAGAGAGG CGGCCTGAGCGAACTGGATAAGGCCGGCTTCATCA AGAGACAGCTGGTGGAAACCCGGCAGATCACAAAG CACGTGGCACAGATCCTGGACTCCCGGATGAACAC TAAGTACGACGAGAATGACAAGCTGATCCGGGAAG TGAAAGTGATCACCCTGAAGTCCAAGCTGGTGTCC GATTTCCGGAAGGATTTCCAGTTTTACAAAGTGCG CGAGATCAACAACTACCACCACGCCCACGACGCCT ACCTGAACGCCGTCGTGGGAACCGCCCTGATCAAA AAGTACCCTAAGCTGGAAAGCGAGTTCGTGTACGG CGACTACAAGGTGTACGACGTGCGGAAGATGATCG CCAAGAGCGAGCAGGAAATCGGCAAGGCTACCGCC AAGTACTTCTTCTACAGCAACATCATGAACTTTTT CAAGACCGAGATTACCCTGGCCAACGGCGAGATCC GGAAGCGGCCTCTGATCGAGACAAACGGCGAAACC GGGGAGATCGTGTGGGATAAGGGCCGGGATTTTGC CACCGTGCGGAAAGTGCTGAGCATGCCCCAAGTGA ATATCGTGAAAAAGACCGAGGTGCAGACAGGCGGC TTCAGCAAAGAGTCTATCCTGCCCAAGAGGAACAG CGATAAGCTGATCGCCAGAAAGAAGGACTGGGACC CTAAGAAGTACGGCGGCTTCGACAGCCCCACCGTG GCCTATTCTGTGCTGGTGGTGGCCAAAGTGGAAAA GGGCAAGTCCAAGAAACTGAAGAGTGTGAAAGAGC TGCTGGGGATCACCATCATGGAAAGAAGCAGCTTC GAGAAGAATCCCATCGACTTTCTGGAAGCCAAGGG CTACAAAGAAGTGAAAAAGGACCTGATCATCAAGC TGCCTAAGTACTCCCTGTTCGAGCTGGAAAACGGC CGGAAGAGAATGCTGGCCTCTGCCGGCGAACTGCA GAAGGGAAACGAACTGGCCCTGCCCTCCAAATATG TGAACTTCCTGTACCTGGCCAGCCACTATGAGAAG CTGAAGGGCTCCCCCGAGGATAATGAGCAGAAACA GCTGTTTGTGGAACAGCACAAGCACTACCTGGACG AGATCATCGAGCAGATCAGCGAGTTCTCCAAGAGA GTGATCCTGGCCGACGCTAATCTGGACAAAGTGCT GTCCGCCTACAACAAGCACCGGGATAAGCCCATCA GAGAGCAGGCCGAGAATATCATCCACCTGTTTACC CTGACCAATCTGGGAGCCCCTGCCGCCTTCAAGTA CTTTGACACCACCATCGACCGGAAGAGGTACACCA GCACCAAAGAGGTGCTGGACGCCACCCTGATCCAC CAGAGCATCACCGGCCTGTACGAGACACGGATCGA CCTGTCTCAGCTGGGAGGCGACAGCCCCAAGAAGA AGAGAAAGGTGGAGGCCAGCTAACATATGATTCGA ATGTCTTTCTTGCGCTATGACACTTCCAGCAAAAG GTAGGGCGGGCTGCGAGACGGCTTCCCGGCGCTGC ATGCAACACCGATGATGCTTCGACCCCCCGAAGCT CCTTCGGGGCTGCATGGGCGCTCCGATGCCGCTCC AGGGCGAGCGCTGTTTAAATAGCCAGGCCCCCGAT TGCAAAGACATTATAGCGAGCTACCAAAGCCATAT TCAAACACCTAGATCACTACCACTTCTACACAGGC CACTCGAGCTTGTGATCGCACTCCGCTAAGGGGGC GCCTCTTCCTCTTCGTTTCAGTCACAACCCGCAAA CATGACACAAGAATCCCTGTTACTTCTCGACCGTA TTGATTCGGATGATTCCTACGCGAGCCTGCGGAAC GACCAGGAATTCTGGGAGGTGAGTCGACGAGCAAG CCCGGCGGATCAGGCAGCGTGCTTGCAGATTTGAC TTGCAACGCCCGCATTGTGTCGACGAAGGCTTTTG GCTCCTCTGTCGCTGTCTCAAGCAGCATCTAACCC TGCGTCGCCGTTTCCATTTGCAGCCGCTGGCCCGC CGAGCCCTGGAGGAGCTCGGGCTGCCGGTGCCGCC GGTGCTGCGGGTGCCCGGCGAGAGCACCAACCCCG TACTGGTCGGCGAGCCCGGCCCGGTGATCAAGCTG TTCGGCGAGCACTGGTGCGGTCCGGAGAGCCTCGC GTCGGAGTCGGAGGCGTACGCGGTCCTGGCGGACG CCCCGGTGCCGGTGCCCCGCCTCCTCGGCCGCGGC GAGCTGCGGCCCGGCACCGGAGCCTGGCCGTGGCC CTACCTGGTGATGAGCCGGATGACCGGCACCACCT GGCGGTCCGCGATGGACGGCACGACCGACCGGAAC GCGCTGCTCGCCCTGGCCCGCGAACTCGGCCGGGT GCTCGGCCGGCTGCACAGGGTGCCGCTGACCGGGA ACACCGTGCTCACCCCCCATTCCGAGGTCTTCCCG GAACTGCTGCGGGAACGCCGCGCGGCGACCGTCGA GGACCACCGCGGGTGGGGCTACCTCTCGCCCCGGC TGCTGGACCGCCTGGAGGACTGGCTGCCGGACGTG GACACGCTGCTGGCCGGCCGCGAACCCCGGTTCGT CCACGGCGACCTGCACGGGACCAACATCTTCGTGG ACCTGGCCGCGACCGAGGTCACCGGGATCGTCGAC TTCACCGACGTCTATGCGGGAGACTCCCGCTACAG CCTGGTGCAACTGCATCTCAACGCCTTCCGGGGCG ACCGCGAGATCCTGGCCGCGCTGCTCGACGGGGCG CAGTGGAAGCGGACCGAGGACTTCGCCCGCGAACT GCTCGCCTTCACCTTCCTGCACGACTTCGAGGTGT TCGAGGAGACCCCGCTGGATCTCTCCGGCTTCACC GATCCGGAGGAACTGGCGCAGTTCCTCTGGGGGCC GCCGGACACCGCCCCCGGCGCCTGATAAGGATCCG GCAAGACTGGCCCCGCTTGGCAACGCAACAGTGAG CCCCTCCCTAGTGTGTTTGGGGATGTGACTATGTA TTCGTGTGTTGGCCAACGGGTCAACCCGAACAGAT TGATACCCGCCTTGGCATTTCCTGTCAGAATGTAA CGTCAGTTGATGGTACT.  For all modified Chlamydomonas reinhardtii cells, Applicants use PCR, SURVEYOR nuclease assay, and DNA sequencing to verify successful modification.

Example 8: Selection of Guide RNA Sequences for Targeting a Given Gene Using a CRISPR-Cas System

Applicants used HumanBody 2.0 expression data from Illumina to calculate for each exon the percent of “constitutiveness”. The term “constitutiveness” as used herein relates to how many times the exon is not spliced out across different tissues. From this anaylsis, Applicants compiled a list of constitutive exons that are expressed across all measured tissues.

Applicants then intersected this data with NCBI CCDS database (available at the website ncbi.nlm.nih.gov/CCDS/) and take CCDS exons which are 98% covered with a constitutive exon from as previously determined.

For each CCDS entry, Applicants took the two earliest constitutive exons. If there are not enough constitutive exons in this gene or no data Applicants added exon 2, 3 or both to get to 2 unique exons.

For each candidate exon Applicants found all the possible S. pyogenes sgRNA guide sequences (or guide sequence) of the form (N)20NGG. Applicants calculated an off target score for each guide sequence as follows:

(a) Applicants used a short-read aligner and mapped each 20mer guide sequence to the genome to find all the sequences that are similar to it allowing up to 3 mismatches. (b) At this point if a guide has a match to a sequence in the genome with zero (perfect match) or one base mismatch it is discarded. (c) For the other guide (closest off target is with two or more mismatches), Applicants calculated the following off target score:

${OS} = {\sum\limits_{{off}\mspace{14mu} {targets}}{\left( {{sum}\mspace{14mu} \min \mspace{14mu} {location}} \right)\left( \frac{D({mm})}{D\left( \max \right)} \right)}}$

where: sum mm location=sum of the mis-match locations from 3′ to 5′. The PAM (NGG) proximal base is 1 and the PAM distal base is 20. D(mm)=distance in bp between mismatch locations. D(max)=maximal possible distance between 2 or 3 mismatches.

Applicants then sort the guide sequences for each gene by off target score, take the two best for each gene up to a off target score of 400. Applicants then iteratively added guide sequences to genes choosing the next best guide sequence for each gene until the whole list of guide sequences contained 65017 guide sequences.

Example 9: Genome Scale CRISPR-Cas9 Knockout Screening in Human Cells

The simplicity of programming the CRISPR-associated nuclease Cas9 to modify specific genomic loci suggests a new way to interrogate gene function on the genome-wide scale. Applicants showed that lentiviral delivery of a genome-scale CRISPR-Cas9 knockout (GeCKO) library targeting 18,080 genes with 64,751 unique guide sequences enables both negative and positive selection screening in human cells. First, Applicants used the GeCKO library to identify genes essential for cell viability in cancer and pluripotent stem cells. Next, in a melanoma model, Applicants screened for candidate genes whose loss is involved in resistance to vemurafenib, a therapeutic that inhibits mutant protein kinase BRAF. Applicants' highest-ranking gene candidates include the previously-validated genes NF1 and MED 12 as well as novel candidate genes (NF2, CUL3, TADA2B and TADA1). Notably, Applicants observed a high level of consistency between independent guide RNAs targeting the same gene and a high rate of validation, demonstrating the promise of genome-scale screening with Cas9.

A major goal since the completion of the Human Genome Project is the functional characterization of all annotated genetic elements in normal biological processes and disease. Genome-scale loss-of-function screens have provided a wealth of information in diverse model systems. In mammalian cells, RNA interference (RNAi) is the predominant method for genome-wide loss-of-function screening, but its utility is limited by the inherent incompleteness of protein depletion by RNAi and confounding off-target effects.

The RNA-guided CRISPR (clustered regularly interspaced short palindrome repeats)-associated nuclease Cas9 provides an effective means of introducing targeted loss-of function mutations at specific sites in the genome. Cas9 can be programmed to induce DNA double strand breaks (DSBs) at specific genomic loci through a synthetic single guide RNA (sgRNA), which when targeted to coding regions of genes can create frame shift indel mutations that result in a loss-of-function allele. Because the targeting specificity of Cas9 is conferred by short guide sequences, which can be easily generated at large scale by array-based oligonucleotide library synthesis, Applicants explored the potential of Cas9 for pooled genome-scale functional screening.

Lentiviral vectors are commonly used for delivery of pooled short hairpin RNAs (shRNAs) in RNAi since they can be easily titrated to control transgene copy number, and are stably maintained as genomic integrants during subsequent cell replication. Therefore Applicants designed a single lentiviral vector to deliver Cas9, a puromycin selection marker, and a sgRNA into target cells (lentiCRISPR, FIGS. 25A and 46). The ability to simultaneously deliver Cas9 and sgRNA through a single vector enables application to any cell type of interest, without the need to first generate cell lines that express Cas9.

To determine the efficacy of gene knockout by lentiCRISPR transduction, Applicants tested six sgRNAs targeting enhanced green fluorescent protein (EGFP) in a HEK293T cell line containing a single-copy of EGFP (FIG. 29). After transduction at a low multiplicity of infection (MOI=0.3) followed by selection with puromycin, lentiCRISPRs abolished EGFP fluorescence in 93±8% (mean±s.d.) of cells after 11 days (FIG. 25B). Deep sequencing of the EGFP locus revealed a 92±9% indel frequency (n≥10⁴ sequencing reads per condition; FIG. 30). In contrast, transduction of cells with lentiviral vectors expressing EGFP-targeting shRNA led to incomplete knockdown of EGFP fluorescence (FIG. 25C).

Given the high efficacy of gene knockout by lentiCRISPR, Applicants tested the feasibility of conducting genome-scale CRISPR knockout (GeCKO) screening with a pooled lentiCRISPR library. Applicants designed a library of sgRNAs targeting 5′ constitutive exons (FIG. 26A) of 18,080 genes in the human genome with an average coverage of 3-4 sgRNAs per gene (Table 1); and each target site was selected to minimize off-target modification as described herein.

To test the efficacy of the full GeCKO library at achieving knockout of endogenous gene targets, Applicants conducted a negative selection screen by profiling the depletion of sgRNAs targeting essential survival genes (FIG. 26A). Applicants transduced the human melanoma cell line A375 and the human stem cell line HUES62 with the GeCKO library at a MOI of 0.3. As expected, deep sequencing (FIG. 31, 32) 14 days post-transduction revealed a significant reduction in the diversity of sgRNAs in the surviving A375 and HUES62 cells (FIG. 26B, C; Wilcoxon rank sum test, p<10¹⁰ for both cell types). Gene set enrichment analysis (GSEA) indicated that most of the depleted sgRNAs targeted essential genes such as ribosomal structural constituents (FIG. 26D, E, and Tables E, F). The overlap in highly depleted genes and functional gene categories between the two cell lines (FIG. 33) indicates that GeCKO can identify essential genes and that enrichment analysis of depleted sgRNAs can pinpoint gene targets in negative selection screens.

TABLE E Gene Set Enrichment Analysis output for negative selection of essential genes in A375 cells after 14 additional days in culture. For the analysis, the ALL Gene Ontology set was used from the Molecular Signatures Database (MSigDB) with a minimum set size of 50 and max set size of 300. RANK AT NAME SIZE ES NES NOMp FDRq FWERp MAX RNA_PROCESSING 165 0.39 5.78 0 0 0 2823 STRUCTURAL_CONSTITUENT_OF_RIBOSOME 71 0.58 5.68 0 0 0 2753 RIBONUCLEOPROTEIN_COMPLEX 138 0.4 5.51 0 0 0 3865 RNA_BINDING 241 0.29 5.21 0 0 0 4664 RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS_AND_ASSEMBLY 81 0.45 4.67 0 0 0 2979 NUCLEOPLASM 271 0.24 4.62 0 0 0 4928 RNA_SPLICING 86 0.42 4.61 0 0 0 2768 NUCLEOLUS 120 0.36 4.56 0 0 0 5363 NUCLEOPLASM_PART 206 0.26 4.41 0 0 0 4047 MRNA_METABOLIC_PROCESS 79 0.42 4.25 0 0 0 4596 MRNA_PROCESSING_GO_0006397 70 0.42 4.13 0 0 0 4596 TRANSLATION 166 0.27 4.09 0 0 0 1815 DNA_METABOLIC_PROCESS 250 0.21 3.86 0 0 0 6569 BIOPOLYMER_CATABOLIC_PROCESS 112 0.29 3.63 0 0 0 6456 CHROMOSOMAL_PART 93 0.32 3.61 0 0 0 4006 PROTEIN_RNA_COMPLEX_ASSEMBLY 62 0.38 3.6 0 0 0 2979 DNA_DIRECTED_RNA_POLYMERASEII_HOLOENZYME 65 0.38 3.6 0 0 0 3367 MACROMOLECULE_CATABOLIC_PROCESS 130 0.26 3.56 0 0 0 6456 ORGANELLE_MEMBRANE 287 0.18 3.56 0 0 0 7993 CHROMOSOME 119 0.28 3.54 0 0 0 3434 DNA_REPLICATION 99 0.3 3.53 0 0 0 3471 MITOCHONDRIAL_PART 138 0.26 3.52 0 0 0 5678 ORGANELLE_ENVELOPE 164 0.23 3.47 0 0 0 6682 STRUCTURAL_MOLECULE_ACTIVITY 218 0.2 3.43 0 0 0 4049 ENVELOPE 164 0.23 3.34 0 0 0 6682 MACROMOLECULAR_COMPLEX_ASSEMBLY 267 0.17 3.21 0 0 0 3419 MITOSIS 80 0.3 3.2 0 0 0 3551 CELLULAR_COMPONENT_ASSEMBLY 284 0.16 3.1 0 0 0 3419 M_PHASE_OF_MITOTIC_CELL_CYCLE 83 0.29 3.08 0 0 0 3551 CELLULAR_MACROMOLECULE_CATABOLIC_PROCESS 99 0.26 3.06 0 0 0 6249 MICROTUBULE_CYTOSKELETON 146 0.22 3.05 0 0 0 4125 CELL_CYCLE_PROCESS 190 0.19 3.01 0 0 0 4125 RESPONSE_TO_ENDOGENOUS_STIMULUS 192 0.18 2.93 0 0 0 7033 RESPONSE_TO_DNA_DAMAGE_STIMULUS 157 0.2 2.92 0 0 0 6569 DNA_REPAIR 121 0.23 2.92 0 0 0 6569 MITOCHONDRIAL_ENVELOPE 93 0.25 2.91 0 0 0 8216 MITOCHONDRIAL_MEMBRANE 82 0.27 2.91 0 0 0 8216 CELL_CYCLE_PHASE 168 0.19 2.88 0 2.82E−05 0.001 4070 M_PHASE 112 0.23 2.86 0 2.75E−05 0.001 3938 PROTEIN_CATABOLIC_PROCESS 67 0.3 2.86 0 2.68E−05 0.001 6456 MICROTUBULE_ORGANIZING_CENTER 65 0.3 2.85 0 2.61E−05 0.001 5445 ORGANELLE_INNER_MEMBRANE 72 0.28 2.78 0 7.79E−05 0.003 8154 MITOCHONDRIAL_INNER_MEMBRANE 64 0.3 2.77 0 7.61E−05 0.003 8154 MITOTIC_CELL_CYCLE 151 0.19 2.76 0 9.95E−05 0.004 2454 DNA_DEPENDENT_DNA_REPLICATION 53 0.31 2.73 0 1.22E−04 0.005 3170 ATPASE_ACTIVITY 110 0.22 2.68 0 1.88E−04 0.008 5581 PROTEIN_FOLDING 55 0.3 2.67 0 2.07E−04 0.009 7936 CYTOSKELETAL_PART 224 0.16 2.64 0 2.03E−04 0.009 4745 CELLULAR_PROTEIN_CATABOLIC_PROCESS 57 0.29 2.6 0 2.22E−04 0.01 6456 NUCLEOSIDE_TRIPHOSPHATASE_ACTIVITY 205 0.15 2.59 0 3.06E−04 0.014 6559 ENDOMEMBRANE_SYSTEM 211 0.15 2.57 0 3.62E−04 0.017 7971 TRANSCRIPTION_FACTOR_COMPLEX 89 0.23 2.57 0 3.55E−04 0.017 9975 PYROPHOSPHATASE_ACTIVITY 219 0.15 2.54 0 4.90E−04 0.024 6559 HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES 221 0.15 2.53 0 5.21E−04 0.026 6559 REGULATION_OF_CELL_CYCLE 175 0.16 2.53 0 5.12E−04 0.026 3551 NUCLEAR_ENVELOPE 72 0.25 2.51 0 6.23E−04 0.032 6682 CENTROSOME 56 0.29 2.51 0 6.12E−04 0.032 5445 INTRACELLULAR_TRANSPORT 271 0.13 2.48 0 7.09E−04 0.038 7734 CATABOLIC_PROCESS 218 0.14 2.45 0 9.14E−04 0.049 3576 LIGASE_ACTIVITY 94 0.22 2.44 0 9.17E−04 0.05 6249 ATPASE_ACTIVITY_COUPLED 91 0.22 2.39 0 0.00138 0.076 5581 CELLULAR_CATABOLIC_PROCESS 206 0.14 2.38 0 0.00141 0.079 3576 MITOCHONDRIAL_MEMBRANE_PART 50 0.27 2.32 0 0.00218 0.121 7993 NUCLEASE_ACTIVITY 55 0.26 2.31 0.002 0.00232 0.129 6720 CHROMOSOME_ORGANIZATION_AND_BIOGENESIS 122 0.18 2.3 0 0.00246 0.14 4623 MACROMOLECULE_LOCALIZATION 230 0.13 2.21 0 0.00434 0.23 7886 NUCLEAR_MEMBRANE 50 0.25 2.04 0.002 0.01183 0.519 6682 REGULATION_OF_PROTEIN_METABOLIC_PROCESS 165 0.14 2.03 0 0.01208 0.531 8311 LIGASE_ACTIVITY_FORMING_CARBON_NITROGEN_BONDS 67 0.2 1.98 0.002 0.01638 0.65 6249 KINASE_BINDING 68 0.2 1.92 0.009 0.02197 0.739 9808 PEPTIDYL_AMINO_ACID_MODIFICATION 62 0.2 1.88 0.011 0.02821 0.827 12915 ESTABLISHMENT_OF_PROTEIN_LOCALIZATION 185 0.12 1.87 0.014 0.02952 0.851 8072 ENZYME_BINDING 174 0.12 1.86 0.008 0.02965 0.855 10013 REGULATION_OF_TRANSCRIPTION_FROM_RNA_POLYMERASE_(—) 283 0.1 1.85 0.006 0.0316 0.875 4713 I_PROMOTER COFACTOR_METABOLIC_PROCESS 54 0.21 1.83 0.008 0.03423 0.894 10520 REGULATION_OF_CELLULAR_PROTEIN_METABOLIC_PROCESS 155 0.12 1.82 0.006 0.03515 0.902 8311 RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_ACTIVITY 179 0.12 1.8 0.012 0.03919 0.929 4869 TRANSFERASE_ACTIVITY_TRANSFERRING_ACYL_GROUPS 59 0.2 1.78 0.006 0.04205 0.94 5002 PROTEIN_LOCALIZATION 209 0.11 1.78 0.016 0.04372 0.948 7886 SMALL_CONJUGATING_PROTEIN_LIGASE_ACTIVITY 51 0.21 1.76 0.025 0.04791 0.962 12441 CYTOSOL 199 0.11 1.75 0.024 0.05038 0.97 4982 REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION_AND_(—) 117 0.14 1.74 0.017 0.05232 0.977 4133 BIOGENESIS POSITIVE_REGULATION_OF_CELLULAR_METABOLIC_PROCESS 224 0.1 1.73 0.034 0.05359 0.981 4250 ACID_AMINO_ACID_LIGASE_ACTIVITY 57 0.2 1.73 0.021 0.05354 0.982 6249 INTRACELLULAR_PROTEIN_TRANSPORT 141 0.12 1.72 0.023 0.05523 0.984 6698 PROTEIN_KINASE_BINDING 60 0.19 1.72 0.022 0.05481 0.984 9808 INTRINSIC_TO_ORGANELLE_MEMBRANE 51 0.2 1.72 0.02 0.05486 0.985 7971 POSITIVE_REGULATION_OF_RNA_METABOLIC_PROCESS 119 0.13 1.71 0.024 0.0559 0.986 4250 INTERPHASE 68 0.17 1.7 0.026 0.05724 0.987 4070 PROTEIN_TRANSPORT 152 0.12 1.69 0.022 0.06056 0.988 8072 ESTABLISHMENT_AND_OR_MAINTENANCE_OF_CHROMATIN_(—) 76 0.17 1.69 0.03 0.06152 0.99 5256 ARCHITECTURE POSITIVE_REGULATION_OF_(—) 153 0.12 1.68 0.031 0.06336 0.992 4250 NUCLEOBASENUCLEOSIDENUCLEOTIDE_AND_(—) NUCLEIC_ACID_METABOLIC_PROCESS ENDOPLASMIC_RETICULUM 278 0.09 1.68 0.026 0.06293 0.992 7817 POSITIVE_REGULATION_OF_TRANSCRIPTIONDNA_(—) 117 0.13 1.67 0.024 0.06531 0.993 4250 DEPENDENT POSITIVE_REGULATION_OF_METABOLIC_PROCESS 230 0.09 1.65 0.028 0.06918 0.997 4250 TRANSCRIPTION_ACTIVATOR_ACTIVITY 170 0.11 1.65 0.039 0.07019 0.998 4537 POSITIVE_REGULATION_OF_TRANSCRIPTION_FROM_RNA_(—) 64 0.17 1.63 0.025 0.07401 0.998 4250 POLYMERASE_II_PROMOTER NUCLEOBASENUCLEOSIDE_AND_NUCLEOTIDE_METABOLIC_(—) 51 0.19 1.63 0.037 0.07477 0.999 5750 PROCESS SMALL_PROTEIN_CONJUGATING_ENZYME_ACTIVITY 52 0.19 1.62 0.027 0.07592 0.999 12441 ENDOPLASMIC_RETICULUM_MEMBRANE 81 0.15 1.61 0.041 0.08117 0.999 6591 POSITIVE_REGULATION_OF_TRANSCRIPTION 143 0.11 1.59 0.051 0.08681 0.999 4250 NUCLEAR_ENVELOPE_ENDOPLASMIC_RETICULUM_NETWORK 90 0.14 1.59 0.039 0.08705 0.999 6591 NUCLEAR_TRANSPORT 86 0.15 1.58 0.04 0.09042 1 7204 ENDOPLASMIC_RETICULUM_PART 92 0.14 1.57 0.042 0.09295 1 6669 TRANSCRIPTION_COACTIVATOR_ACTIVITY 120 0.12 1.57 0.044 0.09258 1 4536 NUCLEOCYTOPLASMIC_TRANSPORT 85 0.14 1.56 0.042 0.09541 1 7204 PROTEIN_C_TERMINUS_BINDING 70 0.16 1.56 0.051 0.09668 1 12272 NUCLEAR_CHROMOSOME 51 0.18 1.54 0.062 0.10619 1 3434 PROTEOLYSIS 184 0.1 1.52 0.066 0.11481 1 6570 CHROMATIN_MODIFICATION 54 0.18 1.51 0.057 0.11578 1 3790 INTERPHASE_OF_MITOTIC_CELL_CYCLE 62 0.16 1.46 0.093 0.1459 1 4070 HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS 263 0.08 1.42 0.08 0.17096 1 10388 GOLGI_APPARATUS_PART 94 0.12 1.41 0.078 0.17588 1 10008 TRANSCRIPTION_COFACTOR_ACTIVITY 219 0.08 1.39 0.095 0.19304 1 4536 PROTEIN_IMPORT 62 0.15 1.39 0.121 0.19213 1 7185 TRANSCRIPTION_FACTOR_BINDING 298 0.07 1.37 0.111 0.20094 1 4802 PROTEIN_HETERODIMERIZATION_ACTIVITY 75 0.13 1.37 0.117 0.20087 1 7886 MICROTUBULE_BASED_PROCESS 76 0.13 1.34 0.146 0.22731 1 2409 POSITIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS 72 0.13 1.32 0.144 0.24339 1 7879 OXIDOREDUCTASE_ACTIVITY 282 0.07 1.32 0.145 0.24362 1 9653 PROTEIN_TARGETING 108 0.11 1.31 0.158 0.24756 1 2572 PHOSPHORIC_ESTER_HYDROLASE_ACTIVITY 149 0.09 1.3 0.149 0.25681 1 10507 GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY 122 0.1 1.29 0.175 0.263 1 10168 GTPASE_ACTIVITY 94 0.11 1.28 0.17 0.27137 1 6559 REGULATION_OF_TRANSLATION 89 0.12 1.28 0.182 0.26987 1 12650 ANION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 59 0.14 1.27 0.155 0.27786 1 14818 INORGANIC_CATION_TRANSMEMBRANE_TRANSPORTER_(—) 56 0.14 1.25 0.203 0.29417 1 6084 ACTIVITY ALCOHOL_METABOLIC_PROCESS 87 0.11 1.24 0.198 0.3057 1 5002 SMALL_GTPASE_REGULATOR_ACTIVITY 67 0.13 1.22 0.212 0.32345 1 9244 CYTOSKELETAL_PROTEIN_BINDING 155 0.08 1.22 0.208 0.32316 1 3830 PROTEIN_DOMAIN_SPECIFIC_BINDING 70 0.13 1.22 0.214 0.32228 1 10281 PROTEIN_DIMERIZATION_ACTIVITY 177 0.08 1.21 0.231 0.32627 1 14919 STRUCTURE_SPECIFIC_DNA_BINDING 54 0.14 1.21 0.243 0.32383 1 7121 GOLGI_APPARATUS 216 0.07 1.21 0.22 0.32532 1 7875 SEQUENCE_SPECIFIC_DNA_BINDING 57 0.13 1.21 0.215 0.3236 1 11740 POSITIVE_REGULATION_OF_CELLULAR_PROTEIN_(—) 70 0.12 1.19 0.247 0.34325 1 7879 METABOLIC_PROCESS CARBOHYDRATE_METABOLIC_PROCESS 177 0.08 1.19 0.217 0.34568 1 10067 GTPASE_REGULATOR_ACTIVITY 122 0.09 1.18 0.232 0.35845 1 9407 SECRETION_BY_CELL 112 0.09 1.17 0.243 0.36174 1 7757 SECRETION 174 0.08 1.16 0.269 0.37594 1 7820 PHOSPHORIC_MONOESTER_HYDROLASE_ACTIVITY 108 0.1 1.16 0.283 0.37476 1 9922 CYTOSKELETON_ORGANIZATION_AND_BIOGENESIS 199 0.07 1.15 0.275 0.38345 1 8398 PROTEIN_COMPLEX_BINDING 53 0.13 1.13 0.298 0.39885 1 14915 RESPONSE_TO_OTHER_ORGANISM 78 0.11 1.12 0.301 0.41053 1 10042 SECRETORY_PATHWAY 80 0.11 1.11 0.285 0.41916 1 6638 PROTEIN_COMPLEX_ASSEMBLY 160 0.07 1.09 0.329 0.45045 1 2284 NUCLEOTIDE_BINDING 213 0.06 1.09 0.334 0.44914 1 5253 GLYCOPROTEIN_BIOSYNTHETIC_PROCESS 74 0.11 1.07 0.347 0.46709 1 9904 RESPONSE_TO_BIOTIC_STIMULUS 112 0.09 1.07 0.358 0.46716 1 11595 DEPHOSPHORYLATION 68 0.11 1.06 0.354 0.48637 1 3576 NEGATIVE_REGULATION_OF_(—) 208 0.06 1.04 0.398 0.51567 1 3307 NUCLEOBASENUCLEOSIDENUCLEOTIDE_AND_(—) NUCLEIC_ACID_METABOLIC_PROCESS CARBOXYLIC_ACID_METABOLIC_PROCESS 176 0.07 1.02 0.409 0.53327 1 13899 RESPONSE_TO_ABIOTIC_STIMULUS 81 0.1 1.01 0.437 0.55167 1 2485 RAS_PROTEIN_SIGNAL_TRANSDUCTION 64 0.11 0.99 0.459 0.56979 1 11509 ACTIN_BINDING 76 0.1 0.99 0.456 0.57185 1 11233 PROTEIN_AMINO_ACID_DEPHOSPHORYLATION 61 0.11 0.99 0.467 0.57088 1 3369 APOPTOTIC_PROGRAM 57 0.11 0.99 0.467 0.5697 1 12804 STRUCTURAL_CONSTITUENT_OF_CYTOSKELETON 54 0.11 0.98 0.464 0.57267 1 5005 ENZYME_INHIBITOR_ACTIVITY 118 0.08 0.97 0.484 0.59056 1 9572 POSITIVE_REGULATION_OF_I_KAPPAB_KINASE_NF_(—) 84 0.09 0.96 0.475 0.59815 1 14222 KAPPAB_CASCADE ORGANIC_ACID_METABOLIC_PROCESS 178 0.06 0.96 0.487 0.59493 1 13899 MONOCARBOXYLIC_ACID_METABOLIC_PROCESS 87 0.09 0.96 0.516 0.59446 1 13681 NEGATIVE_REGULATION_OF_CELLULAR_METABOLIC_PROCESS 255 0.05 0.95 0.5 0.60411 1 3307 GLYCOPROTEIN_METABOLIC_PROCESS 90 0.09 0.95 0.507 0.60702 1 11014 NEGATIVE_REGULATION_OF_METABOLIC_PROCESS 257 0.05 0.94 0.502 0.61476 1 3307 SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION 85 0.09 0.94 0.499 0.61255 1 11509 PROTEIN_HOMODIMERIZATION_ACTIVITY 118 0.07 0.94 0.515 0.6163 1 14919 POSITIVE_REGULATION_OF_SIGNAL_TRANSDUCTION 120 0.07 0.94 0.53 0.61278 1 15308 RESPONSE_TO_RADIATION 55 0.11 0.93 0.527 0.61353 1 2360 CELLULAR_CARBOHYDRATE_METABOLIC_PROCESS 124 0.07 0.91 0.552 0.64116 1 4663 REGULATION_OF_I_KAPPAB_KINASE_NF_KAPPAB_CASCADE 90 0.08 0.91 0.565 0.65121 1 15690 LIPID_BIOSYNTHETIC_PROCESS 96 0.08 0.88 0.581 0.69681 1 10784 PURINE_NUCLEOTIDE_BINDING 200 0.05 0.86 0.661 0.7253 1 15565 PURINE_RIBONUCLEOTIDE_BINDING 194 0.05 0.84 0.663 0.75173 1 5186 AMINO_ACID_METABOLIC_PROCESS 77 0.08 0.82 0.691 0.77186 1 12986 PHOSPHOPROTEIN_PHOSPHATASE_ACTIVITY 79 0.08 0.82 0.721 0.76882 1 3369 ATP_BINDING 149 0.05 0.8 0.729 0.79992 1 15510 ADENYL_NUCLEOTIDE_BINDING 162 0.05 0.78 0.752 0.81705 1 15539 ELECTRON_TRANSPORT_GO_0006118 51 0.09 0.76 0.766 0.85094 1 9279 MULTI_ORGANISM_PROCESS 153 0.05 0.75 0.792 0.857 1 13249 ADENYL_RIBONUCLEOTIDE_BINDING 156 0.05 0.74 0.794 0.87127 1 15539 REGULATION_OF_BINDING 56 0.08 0.74 0.782 0.86663 1 5256 IDENTICAL_PROTEIN_BINDING 297 0.04 0.73 0.819 0.8703 1 14671 REGULATION_OF_GROWTH 54 0.08 0.71 0.824 0.89318 1 9818 OXIDOREDUCTASE_ACTIVITY_ACTING_ON_CH_OH_(—) 61 0.08 0.71 0.83 0.89082 1 2727 GROUP_OF_DONORS ELECTRON_CARRIER_ACTIVITY 78 0.07 0.7 0.867 0.90169 1 13510 GROWTH 72 0.07 0.67 0.883 0.9323 1 2784 CYSTEINE_TYPE_PEPTIDASE_ACTIVITY 54 0.08 0.66 0.87 0.93021 1 7915 HEMOPOIESIS 71 0.07 0.65 0.905 0.94316 1 9936 PROTEIN_AMINO_ACID_PHOSPHORYLATION 268 0.03 0.64 0.89 0.94752 1 6898 TRANSITION_METAL_ION_BINDING 106 0.05 0.62 0.933 0.95526 1 4837 ACTIN_CYTOSKELETON 125 0.04 0.56 0.978 0.99424 1 10554 AMINO_ACID_AND_DERIVATIVE_METABOLIC_PROCESS 99 0.05 0.55 0.96 0.99288 1 13079 NEGATIVE_REGULATION_OF_RNA_METABOLIC_PROCESS 129 0.04 0.55 0.972 0.98941 1 7189 REGULATION_OF_RESPONSE_TO_STIMULUS 59 0.06 0.51 0.99 0.99725 1 7791 ENZYME_ACTIVATOR_ACTIVITY 120 0.04 0.49 0.996 0.9967 1 13202 NITROGEN_COMPOUND_METABOLIC_PROCESS 151 0.03 0.49 0.992 0.99283 1 16617

TABLE F Gene Set Enrichment Analysis output for negative selection of essential genes in HUES62 hES cells after 14 additional days in culture. For the analysis, the ALL Gene Ontology set was used from from the Moleular Signatures Database (MSigDB) with a minimum set size of 50 and max set size of 300. RANK AT NAME SIZE ES NES NOMp FDRq FWERp MAX RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS_AND_ASSEMBLY 73 0.2 2.3 0 0.142 0.121 4298 RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_ACTIVITY 162 0.1 2.1 0 0.222 0.329 3199 RNA_SPLICING 76 0.2 2.1 0.006 0.204 0.416 6793 RNA_PROCESSING 144 0.1 2 0.004 0.219 0.534 5451 PROTEIN_RNA_COMPLEX_ASSEMBLY 57 0.2 2 0.006 0.189 0.563 4298 MITOSIS 71 0.2 1.9 0.008 0.244 0.716 5678 M_PHASE_OF_MITOTIC_CELL_CYCLE 74 0.2 1.9 0.01 0.255 0.788 5678 REPRODUCTIVE_PROCESS 137 0.1 1.8 0.019 0.414 0.947 6727 MITOTIC_CELL_CYCLE 137 0.1 1.8 0.019 0.403 0.958 8284 REGULATION_OF_CELL_CYCLE 157 0.1 1.7 0.039 0.647 0.995 9226 RIBONUCLEOPROTEIN_COMPLEX 115 0.1 1.6 0.043 0.717 0.998 6653 MACROMOLECULAR_COMPLEX_ASSEMBLY 242 0.1 1.6 0.03 0.691 1 4562 TRANSLATION 147 0.1 1.6 0.05 0.671 1 7108 DNA_DIRECTED_RNA_POLYMERASEII_HOLOENZYME 57 0.2 1.6 0.049 0.631 1 5123 CHROMOSOMAL_PART 77 0.1 1.6 0.063 0.701 1 8719 CELLULAR_COMPONENT_ASSEMBLY 257 0.1 1.5 0.062 0.688 1 4562 RNA_BINDING 216 0.1 1.5 0.056 0.696 1 5522 M_PHASE 101 0.1 1.5 0.08 0.687 1 8489 MRNA_PROCESSING_GO_0006397 63 0.2 1.5 0.068 0.663 1 4298 REPRODUCTION 226 0.1 1.5 0.053 0.632 1 6759 MRNA_METABOLIC_PROCESS 71 0.1 1.5 0.086 0.732 1 6950 REGULATION_OF_KINASE_ACTIVITY 133 0.1 1.5 0.083 0.733 1 7168 ENZYME_BINDING 154 0.1 1.4 0.087 0.735 1 10360 REGULATION_OF_PROTEIN_KINASE_ACTIVITY 131 0.1 1.4 0.1 0.773 1 7168 NUCLEOLUS 94 0.1 1.4 0.113 0.764 1 7137 TRANSCRIPTION_FACTOR_COMPLEX 81 0.1 1.4 0.113 0.742 1 8392 CHROMOSOME 102 0.1 1.4 0.091 0.721 1 2248 STRUCTURAL_CONSTITUENT_OF_RIBOSOME 60 0.2 1.4 0.098 0.709 1 10943 CELL_ACTIVATION 71 0.1 1.4 0.114 0.701 1 6829 CELL_CYCLE_PHASE 153 0.1 1.4 0.093 0.713 1 8333 POSITIVE_REGULATION_OF_TRANSCRIPTION 131 0.1 1.4 0.11 0.701 1 8116 TRANSMISSION_OF_NERVE_IMPULSE 170 0.1 1.4 0.12 0.699 1 11366 APOPTOTIC_PROGRAM 51 0.2 1.4 0.12 0.692 1 5013 DNA_METABOLIC_PROCESS 219 0.1 1.4 0.117 0.676 1 9608 POSITIVE_REGULATION_OF_CELLULAR_METABOLIC_PROCESS 204 0.1 1.3 0.146 0.745 1 8687 MICROTUBULE_CYTOSKELETON 132 0.1 1.3 0.142 0.739 1 1731 KINASE_BINDING 61 0.1 1.3 0.142 0.726 1 10359 REGULATION_OF_TRANSFERASE_ACTIVITY 137 0.1 1.3 0.138 0.711 1 7168 LYMPHOCYTE_ACTIVATION 56 0.1 1.3 0.151 0.693 1 6829 MACROMOLECULE_CATABOLIC_PROCESS 116 0.1 1.3 0.145 0.68 1 13196 LEUKOCYTE_ACTIVATION 64 0.1 1.3 0.17 0.71 1 6829 POSITIVE_REGULATION_OF_METABOLIC_PROCESS 210 0.1 1.3 0.181 0.716 1 8687 PROTEIN_KINASE_BINDING 53 0.2 1.3 0.142 0.703 1 7909 RESPONSE_TO_ENDOGENOUS_STIMULUS 174 0.1 1.3 0.163 0.693 1 9799 CELLULAR_MACROMOLECULE_CATABOLIC_PROCESS 87 0.1 1.3 0.156 0.691 1 12929 BIOPOLYMER_CATABOLIC_PROCESS 103 0.1 1.3 0.185 0.697 1 6589 POSITIVE_REGULATION_OF_(—) 141 0.1 1.3 0.18 0.692 1 8116 NUCLEOBASENUCLEOSIDENUCLEOTIDE_AND_(—) NUCLEIC_ACID_METABOLIC_PROCESS ANION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 56 0.1 1.3 0.177 0.702 1 6320 CELL_PROJECTION 94 0.1 1.3 0.2 0.691 1 7993 SYNAPTIC_TRANSMISSION 156 0.1 1.2 0.193 0.767 1 11366 CARBOHYDRATE_BINDING 61 0.1 1.2 0.192 0.757 1 2825 CYTOKINE_PRODUCTION 65 0.1 1.2 0.189 0.752 1 9817 PROTEIN_CATABOLIC_PROCESS 61 0.1 1.2 0.222 0.758 1 13196 PHOSPHORIC_ESTER_HYDROLASE_ACTIVITY 141 0.1 1.2 0.2 0.754 1 12864 PROTEIN_TYROSINE_KINASE_ACTIVITY 54 0.1 1.2 0.198 0.745 1 5783 CALCIUM_ION_BINDING 89 0.1 1.2 0.215 0.77 1 7829 PHOSPHOTRANSFERASE_ACTIVITY_ALCOHOL_GROUP_AS_(—) 299 0.1 1.2 0.238 0.764 1 7371 ACCEPTOR REGULATION_OF_CELL_PROLIFERATION 273 0.1 1.2 0.235 0.774 1 8412 CENTRAL_NERVOUS_SYSTEM_DEVELOPMENT 112 0.1 1.2 0.256 0.821 1 7866 REGULATION_OF_SIGNAL_TRANSDUCTION 195 0.1 1.2 0.246 0.831 1 9366 POSITIVE_REGULATION_OF_TRANSCRIPTIONDNA_(—) 108 0.1 1.2 0.247 0.82 1 8055 DEPENDENT POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS 195 0.1 1.2 0.259 0.834 1 12108 POSITIVE_REGULATION_OF_RNA_METABOLIC_PROCESS 110 0.1 1.2 0.279 0.829 1 8055 PHOSPHORIC_MONOESTER_HYDROLASE_ACTIVITY 103 0.1 1.1 0.275 0.826 1 12864 NEGATIVE_REGULATION_OF_CELL_PROLIFERATION 135 0.1 1.1 0.279 0.818 1 8723 TRANSCRIPTION_ACTIVATOR_ACTIVITY 156 0.1 1.1 0.297 0.829 1 10875 DNA_REPLICATION 82 0.1 1.1 0.306 0.843 1 6359 MONOCARBOXYLIC_ACID_METABOLIC_PROCESS 77 0.1 1.1 0.3 0.839 1 13160 NUCLEOPLASM_PART 184 0.1 1.1 0.311 0.83 1 2383 POSITIVE_REGULATION_OF_TRANSFERASE_ACTIVITY 71 0.1 1.1 0.296 0.818 1 5202 NEGATIVE_REGULATION_OF_METABOLIC_PROCESS 232 0.1 1.1 0.311 0.831 1 5603 MAPKKK_CASCADE_GO_0000165 87 0.1 1.1 0.339 0.835 1 5783 MICROTUBULE_ORGANIZING_CENTER 56 0.1 1.1 0.321 0.831 1 1731 NEGATIVE_REGULATION_OF_CELLULAR_METABOLIC_(—) 230 0.1 1.1 0.314 0.822 1 5603 PROCESS CELL_CYCLE_GO_0007049 273 0.1 1.1 0.322 0.815 1 8333 PHOSPHORYLATION 282 0.1 1.1 0.318 0.807 1 11887 CELLULAR_PROTEIN_CATABOLIC_PROCESS 51 0.1 1.1 0.341 0.821 1 12860 MEMBRANE_ORGANIZATION_AND_BIOGENESIS 124 0.1 1.1 0.329 0.818 1 3729 PROTEINACEOUS_EXTRACELLULAR_MATRIX 85 0.1 1.1 0.327 0.84 1 12100 PROTEIN_DIMERIZATION_ACTIVITY 160 0.1 1.1 0.351 0.837 1 9757 G_PROTEIN_SIGNALING_COUPLED_TO_CAMP_NUCLEOTIDE_(—) 58 0.1 1.1 0.365 0.831 1 4757 SECOND_MESSENGER ACID_AMINO_ACID_LIGASE_ACTIVITY 53 0.1 1.1 0.364 0.83 1 5009 EXTRACELLULAR_MATRIX 85 0.1 1.1 0.335 0.828 1 12100 NEGATIVE_REGULATION_OF_CELL_CYCLE 67 0.1 1.1 0.385 0.837 1 13433 DNA_REPAIR 108 0.1 1.1 0.343 0.827 1 9370 VESICLE_MEDIATED_TRANSPORT 175 0.1 1.1 0.375 0.826 1 3962 ORGANELLE_MEMBRANE 262 0.1 1.1 0.335 0.823 1 11505 PURINE_NUCLEOTIDE_BINDING 183 0.1 1.1 0.349 0.824 1 5664 CYTOSKELETAL_PART 206 0.1 1 0.372 0.819 1 1731 CYTOSOL 183 0.1 1 0.369 0.828 1 12199 PURINE_RIBONUCLEOTIDE_BINDING 178 0.1 1 0.398 0.825 1 5664 SEXUAL_REPRODUCTION 117 0.1 1 0.396 0.842 1 12380 ZINC_ION_BINDING 76 0.1 1 0.395 0.836 1 2628 CELL_CYCLE_PROCESS 172 0.1 1 0.416 0.864 1 8333 IDENTICAL_PROTEIN_BINDING 265 0.1 1 0.421 0.861 1 2850 LIGASE_ACTIVITY_FORMING_CARBON_NITROGEN_BONDS 63 0.1 1 0.441 0.855 1 5120 ANTI_APOPTOSIS 105 0.1 1 0.444 0.852 1 4654 SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION 78 0.1 1 0.453 0.854 1 10865 CAMP_MEDIATED_SIGNALING 59 0.1 1 0.418 0.857 1 4757 REGULATION_OF_PROTEIN_METABOLIC_PROCESS 154 0.1 1 0.467 0.855 1 3729 TRANSCRIPTION_COACTIVATOR_ACTIVITY 109 0.1 1 0.477 0.869 1 12523 NUCLEAR_ENVELOPE 62 0.1 1 0.464 0.871 1 2228 OXIDOREDUCTASE_ACTIVITY 257 0.1 1 0.458 0.871 1 6094 ENZYME_REGULATOR_ACTIVITY 279 0 1 0.478 0.884 1 12824 EXTRACELLULAR_MATRIX_PART 50 0.1 1 0.498 0.881 1 12058 CATABOLIC_PROCESS 200 0.1 1 0.49 0.894 1 13541 NEUROGENESIS 83 0.1 0.9 0.526 0.91 1 12169 CYTOSKELETON_ORGANIZATION_AND_BIOGENESIS 182 0.1 0.9 0.508 0.912 1 8813 MACROMOLECULE_BIOSYNTHETIC_PROCESS 276 0 0.9 0.511 0.912 1 12108 CARBOHYDRATE_METABOLIC_PROCESS 160 0.1 0.9 0.509 0.91 1 12203 ACTIN_CYTOSKELETON_ORGANIZATION_AND_BIOGENESIS 89 0.1 0.9 0.508 0.903 1 8813 PROTEIN_DOMAIN_SPECIFIC_BINDING 64 0.1 0.9 0.523 0.908 1 12290 CATION_BINDING 181 0.1 0.9 0.539 0.905 1 12366 PROTEIN_C_TERMINUS_BINDING 61 0.1 0.9 0.532 0.907 1 5785 TRANSCRIPTION_FACTOR_BINDING 271 0 0.9 0.543 0.9 1 11687 RAS_PROTEIN_SIGNAL_TRANSDUCTION 58 0.1 0.9 0.537 0.894 1 10865 LYASE_ACTIVITY 65 0.1 0.9 0.579 0.931 1 9672 NEGATIVE_REGULATION_OF_(—) 186 0.1 0.9 0.57 0.926 1 3709 NUCLEOBASENUCLEOSIDENUCLEOTIDE_AND_(—) NUCLEIC_ACID_METABOLIC_PROCESS PROTEIN_HOMODIMERIZATION_ACTIVITY 108 0.1 0.9 0.578 0.922 1 11217 ORGAN_MORPHOGENESIS 128 0.1 0.9 0.582 0.928 1 12177 SOLUBLE_FRACTION 148 0.1 0.9 0.579 0.929 1 6965 INTERPHASE_OF_MITOTIC_CELL_CYCLE 57 0.1 0.9 0.601 0.924 1 8280 REGULATION_OF_CATALYTIC_ACTIVITY 240 0 0.9 0.617 0.921 1 5348 CELLULAR_CATABOLIC_PROCESS 188 0.1 0.9 0.616 0.919 1 12351 POSITIVE_REGULATION_OF_CELLULAR_PROTEIN_(—) 65 0.1 0.9 0.598 0.916 1 8687 METABOLIC_PROCESS STRUCTURAL_MOLECULE_ACTIVITY 192 0.1 0.9 0.613 0.91 1 12175 REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS 136 0.1 0.9 0.603 0.912 1 12283 TRANSCRIPTION_COFACTOR_ACTIVITY 196 0.1 0.9 0.597 0.927 1 12429 LIPID_BINDING 79 0.1 0.9 0.63 0.923 1 12751 REGULATION_OF_MAP_KINASE_ACTIVITY 54 0.1 0.9 0.614 0.921 1 3169 POSITIVE_REGULATION_OF_I_KAPPAB_KINASE_NF_(—) 76 0.1 0.9 0.603 0.919 1 9729 KAPPAB_CASCADE POSITIVE_REGULATION_OF_PROTEIN_METABOLIC_PROCESS 67 0.1 0.9 0.623 0.927 1 8687 PROTEIN_AMINO_ACID_PHOSPHORYLATION 251 0 0.9 0.635 0.925 1 11887 HYDROLASE_ACTIVITY_ACTING_ON_ESTER_BONDS 244 0 0.8 0.645 0.923 1 13028 CYTOPLASMIC_VESICLE 105 0.1 0.8 0.637 0.919 1 13797 REGULATION_OF_I_KAPPAB_KINASE_NF_KAPPAB_CASCADE 81 0.1 0.8 0.635 0.927 1 9729 SKELETAL_DEVELOPMENT 96 0.1 0.8 0.639 0.935 1 11294 SMALL_GTPASE_REGULATOR_ACTIVITY 62 0.1 0.8 0.673 0.945 1 12082 REGULATION_OF_BINDING 52 0.1 0.8 0.701 0.939 1 12761 ENDOMEMBRANE_SYSTEM 190 0.1 0.8 0.687 0.946 1 11505 CYTOPLASMIC_MEMBRANE_BOUND_VESICLE 102 0.1 0.8 0.709 0.949 1 13797 TRANSITION_METAL_ION_BINDING 94 0.1 0.8 0.708 0.946 1 2628 MUSCLE_DEVELOPMENT 88 0.1 0.8 0.696 0.94 1 12772 GAMETE_GENERATION 96 0.1 0.8 0.695 0.94 1 12659 RESPONSE_TO_DNA_DAMAGE_STIMULUS 140 0.1 0.8 0.758 0.941 1 9799 GTPASE_REGULATOR_ACTIVITY 111 0.1 0.8 0.722 0.938 1 5348 LIGASE_ACTIVITY 86 0.1 0.8 0.739 0.947 1 5410 NEGATIVE_REGULATION_OF_TRANSCRIPTION 171 0.1 0.8 0.734 0.942 1 3709 PROTEIN_KINASE_ACTIVITY 256 0 0.8 0.765 0.944 1 7338 STRUCTURAL_CONSTITUENT_OF_CYTOSKELETON 50 0.1 0.8 0.743 0.944 1 2346 VACUOLE 62 0.1 0.8 0.727 0.945 1 6726 NEGATIVE_REGULATION_OF_APOPTOSIS 130 0.1 0.8 0.759 0.94 1 4654 SECRETION 158 0.1 0.8 0.756 0.936 1 11635 REGULATION_OF_MOLECULAR_FUNCTION 283 0 0.8 0.752 0.937 1 5603 REGULATION_OF_TRANSPORT 61 0.1 0.8 0.768 0.943 1 14839 REGULATION_OF_TRANSLATION 82 0.1 0.8 0.778 0.942 1 8502 PROTEIN_IMPORT 53 0.1 0.8 0.765 0.939 1 412 ION_BINDING 232 0 0.8 0.759 0.942 1 11557 ORGANELLE_ENVELOPE 147 0.1 0.8 0.782 0.937 1 3663 GROWTH 67 0.1 0.8 0.771 0.934 1 12240 FATTY_ACID_METABOLIC_PROCESS 56 0.1 0.8 0.787 0.934 1 12183 NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS 173 0 0.7 0.794 0.94 1 4654 I_KAPPAB_KINASE_NF_KAPPAB_CASCADE 99 0.1 0.7 0.808 0.938 1 14020 NEGATIVE_REGULATION_OF_PROGRAMMED_CELL_DEATH 131 0.1 0.7 0.807 0.935 1 4654 ENVELOPE 147 0.1 0.7 0.788 0.929 1 3663 PROTEIN_KINASE_CASCADE 258 0 0.7 0.842 0.948 1 13666 TRANSCRIPTION_COREPRESSOR_ACTIVITY 78 0.1 0.7 0.826 0.945 1 3220 REGULATION_OF_TRANSCRIPTION_FROM 255 0 0.7 0.806 0.949 1 3002 RNA_POLYMERASE_II_PROMOTER MEMBRANE_BOUND_VESICLE 104 0.1 0.7 0.85 0.95 1 11308 ENZYME_ACTIVATOR_ACTIVITY 111 0.1 0.7 0.852 0.948 1 12334 TRANSFERASE_ACTIVITY_TRANSFERRING_HEXOSYL_GROUPS 75 0.1 0.7 0.84 0.955 1 12906 TRANSCRIPTION_REPRESSOR_ACTIVITY 131 0.1 0.7 0.853 0.958 1 3240 EXTRACELLULAR_REGION_PART 294 0 0.7 0.868 0.956 1 12644 RECEPTOR_COMPLEX 51 0.1 0.7 0.868 0.976 1 2182 NEGATIVE_REGULATION_OF_CATALYTIC_ACTIVITY 64 0.1 0.7 0.903 0.977 1 4937 MITOCHONDRIAL_PART 125 0 0.6 0.928 0.986 1 11489 PROTEIN_COMPLEX_ASSEMBLY 146 0 0.6 0.902 0.982 1 4562 MICROTUBULE_BASED_PROCESS 74 0.1 0.6 0.893 0.978 1 12093 NUCLEAR_ENVELOPE_ENDOPLASMIC_RETICULUM_NETWORK 82 0.1 0.6 0.91 0.994 1 3200 ORGANELLE_INNER_MEMBRANE 65 0.1 0.6 0.93 0.989 1 3663 TRANSFERASE_ACTIVITY_TRANSFERRING_ACYL_GROUPS 54 0.1 0.6 0.939 0.992 1 10232 REGULATION_OF_GROWTH 51 0.1 0.6 0.922 0.989 1 11803 IMMUNE_SYSTEM_DEVELOPMENT 75 0.1 0.6 0.957 0.984 1 14325 ATPASE_ACTIVITY_COUPLED 82 0.1 0.6 0.948 0.982 1 13690 POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY 142 0 0.6 0.935 0.978 1 5324 ACTIN_FILAMENT_BASED_PROCESS 99 0.1 0.6 0.959 0.984 1 8813 POSITIVE_REGULATION_OF_TRANSCRIPTION_FROM_RNA_(—) 59 0.1 0.6 0.959 0.986 1 8009 POLYMERASE_II_PROMOTER HEMOPOIETIC_OR_LYMPHOID_ORGAN_DEVELOPMENT 71 0.1 0.6 0.968 0.982 1 14325 HEMOPOIESIS 69 0.1 0.6 0.976 0.987 1 6829 INTERPHASE 63 0.1 0.6 0.978 0.983 1 8280 ACTIN_BINDING 70 0.1 0.5 0.996 0.995 1 3563 ENDOPLASMIC_RETICULUM 253 0 0.5 0.986 0.992 1 15352

To test the efficacy of GeCKO for positive selection, Applicants sought to identify gene knockouts that result in resistance to the BRAF protein kinase inhibitor vemurafenib (PLX) in melanoma (FIG. 27A). Exposure to PLX resulted in growth arrest of transduced A375 cells, which harbor the V600E gain-of-function BRAF mutation (FIG. 27B), therefore enabling the enrichment of a small group of cells that had been rendered drug-resistant by Cas9:sgRNA-mediated modification. After 14 days of PLX treatment, the sgRNA distribution was significantly different when compared with vehicle-treated cells (FIG. 27C; Wilcoxon rank-sum test, p<10⁻¹⁰) and clustered separately from all other conditions (FIGS. 27D and 34).

For a set of genes, Applicants found enrichment of multiple sgRNAs that target each gene after 14 days of PLX treatment (FIG. 27E), suggesting that loss of these particular genes contributes to PLX resistance. Applicants used the RNAi Gene Enrichment Ranking (RIGER) algorithm to rank screening hits by the consistent enrichment among multiple sgRNAs targeting the same gene (FIGS. 27F, 45). Applicants' highest ranking genes contained previously reported candidates NF1 and MED12 and also several previously unknown genes, including neurofibromin 2 (NF2), Cullin 3 E3 ligase (CUL3), and members of the STAGA histone acetyltransferase complex (TADA1 and TADA2B). These candidates yielded new testable hypotheses regarding PLX resistance mechanisms. For example, NF1 and NF2, although unrelated in sequence, are each mutated in similar but distinct forms of neurofibromatosis. In addition, epigenetic dysregulation resulting from mutations in the mechanistically related STAGA and Mediator complexes may have a role in acquired drug resistance. All of these hits were also identified through a second independent transduction (FIGS. 35 and 36, and Tables G and H).

TABLE G Output of the RIGER algorithm for the initial A375 PLX screen comparing PLX (mean of the two replicates at day 14) to DMSO control (mean of the two replicates at day 14). The weighted sum method was used to convert sgRNAs to genes. Genes are sorted by RIGER rank. # Hairpin Gene p-value Gene Hairpins Hairpins ranks NES rank p-value rank NF2 s_36796, 4 58, 415, 31, 22 8E−04 1 0.000004 2 s_36797, s_36798, s_36799 MED12 s_33340, 4 53, 38, 45, 67 0.001 2 0.000004 3 s_33341, s_33342, s_33343 CUL3 s_14311, 6 49523, 41, 17, 0.001 3 0.000006 5 s_14312, 44, 6188, 18040 s_14313, s_14314, s_14315, s_14316 CLDN10 s_12138, 4 23, 24918, 69, 0.002 4 0.000005 4 s_12139, 4914 s_12140, s_12141 NF1 s_36794, 2 130, 1 0.002 5 0.000001 1 s_36795 TADA1 s_55204, 4 137, 93, 0.003 6 0.000035 6 s_55205, 5672, 927 s_55206, s_55207 TADA2B s_55211, 3 127, 249, 0.005 7 0.000046 7 s_55212, 429 s_55213 SPECC1 s_53443, 9 145, 26652, 0.005 8 0.000146 11 s_53444, 43674, 56582, s_53445, 58227, 59830, s_53446, 20, 22519, s_53447, 21861 s_53448, s_53449, s_53450, s_53451 CCDC101 s_9430, 3 333, 492, 198 0.007 9 0.000082 8 s_9431, s_9432 ALG3 s_2023, 4 2441, 297, 0.007 10 0.000118 9 s_2024, 138, 22771 s_2025, s_2026 P4HB s_39947, 3 59088, 30, 0.01 11 0.000189 12 s_39948, 576 s_39949 EED s_17448, 4 2886, 293, 0.011 12 0.000313 15 s_17449, 443, 16470 s_17450, s_17451 TAF6L s_55283, 3 1977, 330, 532 0.011 13 0.000234 13 s_55284, s_55285 MED15 s_33355, 4 285, 504, 0.012 14 0.000382 17 s_33356, 3489, 542 s_33357, s_33358 NPPC s_37703, 6 204, 6109, 0.012 15 0.000575 24 s_37704, 39836, 60416, s_37705, 10125, 403 s_37706, s_37707, s_37708 TAF5L s_55276, 2 199, 831 0.012 16 0.000141 10 s_55277 PGD s_41483, 3 624, 484, 0.013 17 0.000349 16 s_41484, 1163 s_41485 LGALS4 s_30886, 4 33, 678, 0.014 18 0.00051 22 s_30887, 16507, 14753 s_30888, s_30889 TAOK1 s_55349, 3 696, 505, 0.014 19 0.000429 19 s_55350, 5374 s_55351 CD320 s_10386, 6 17447, 182, 0.014 20 0.000824 30 s_10387, 35806, 50696, s_10388, 49163, 488 s_10389, s_10390, s_10391 CCNC s_10026, 5 52916, 817, 0.015 21 0.000735 25 s_10027, 518, 51901, s_10028, 385 s_10029, s_10030 SMARCB1 s_52518, 3 614, 733, 0.016 22 0.000501 21 s_52519, 2280 s_52520 ASIC1 s_3947, 6 605, 53882, 0.016 23 0.001042 34 s_3948, 17965, 48, s_3949, 12823, 15216 s_3950, s_3951, s_3952 MED19 s_33371, 4 298, 3666, 0.017 24 0.000754 27 s_33372, 7614, 748 s_33373, s_33374 GADD45GIP1 s_22055, 4 832, 124, 0.017 25 0.000795 29 s_22056, 9275, 1307 s_22057, s_22058 MED23 s_33386, 2 430, 1171 0.018 26 0.000301 14 s_33387 ZDHHC15 s_62858, 4 60, 48709, 0.019 27 0.000988 33 s_62859, 953, 52940 s_62860, s_62861 TWF2 s_59891, 6 25884, 211, 0.019 28 0.001489 41 s_59892, 11866, 668, s_59893, 55063, 18294 s_59894, s_59895, s_59896 ADRA2B s_1352, 3 55393, 482, 0.021 29 0.000873 31 s_1353, 1091 s_1354 PDC s_40830, 6 56956, 242, 0.021 30 0.001707 50 s_40831, 720, 49078, s_40832, 43057, 3523 s_40833, s_40834, s_40835 KCTD10 s_28876, 3 1094, 3568, 0.021 31 0.000896 32 s_28877, 534 s_28878 MFSD9 s_33784, 2 1176, 1027 0.021 32 0.000419 18 s_33785 TXNDC17 s_59941, 4 25655, 509, 0.022 33 0.00128 38 s_59942, 935, 6800 s_59943, s_59944 MED16 s_33359, 4 912, 608, 0.022 34 0.001299 40 s_33360, 20030, 4476 s_33361, s_33362 TADA3 s_55214, 2 1504, 234 0.022 35 0.000455 20 s_55215 PDCD10 s_40840, 5 30804, 804, 0.023 36 0.001744 51 s_40841, 1252, 20846, s_40842, 561 s_40843, s_40844 TNFRSF17 s_58081, 4 1184, 29, 0.023 37 0.001491 42 s_58082, 50083, 12376 s_58083, s_58084 DARS s_14981, 6 54968, 41173, 0.023 38 0.002111 61 s_14982, 736, 52808, s_14983, 20070, 493 s_14984, s_14985, s_14986 ELMOD1 s_18007, 2 221, 1617 0.024 39 0.000523 23 s_18008 ARID1A s_3477, 4 53744, 167, 0.024 40 0.001505 43 s_3478, 1145, 4655 s_3479, s_3480 GNB2L1 s_23260, 4 12534, 598, 0.024 41 0.001556 44 s_23261, 1022, 8784 s_23262, s_23263 SCPEP1 s_49407, 4 949, 61876, 0.024 42 0.001613 45 s_49408, 883, 50303 s_49409, s_49410 KEAP1 s_29029, 4 4069, 1053, 0.025 43 0.001632 47 s_29030, 43892, 601 s_29031, s_29032 NCOR2 s_36330, 4 991, 11014, 0.025 44 0.00166 48 s_36331, 20939, 822 s_36332, s_36333 OR2T33 s_39119, 3 1342, 9376, 0.025 45 0.001231 37 s_39120, 500 s_39121 BCL2L12 s_5187, 4 1605, 711, 0.025 46 0.001761 53 s_5188, 5895, 1061 s_5189, s_5190 SPOPL s_53635, 3 1325, 664, 0.026 47 0.001289 39 s_53636, 56183 s_53637 FGGY s_21004, 6 852, 9579, 0.026 48 0.002495 68 s_21005, 32124, 29464, s_21006, 27460, 388 s_21007, s_21008, s_21009 CA7 s_8596, 6 273, 62443, 0.026 49 0.002567 69 s_8597, 30916, 21259, s_8598, 7063, 905 s_8599, s_8600, s_8601 JMJD4 s_28292, 6 975, 19283, 0.026 50 0.002601 70 s_28293, 81, 29765, s_28294, 46303, 47416 s_28295, s_28296, s_28297 MYO9B s_35776, 4 1257, 326, 0.027 51 0.001952 57 s_35777, 21804, 23954 s_35778, s_35779 FAM19A4 s_19778, 6 62838, 909, 0.027 52 0.002769 76 s_19779, 383, 23595, s_19780, 32237, 42288 s_19781, s_19782, s_19783 EBF4 s_17294, 4 64198, 1219, 0.027 53 0.002002 59 s_17295, 506, 15439 s_17296, s_17297 TTC4 s_59623, 5 1161, 52043, 0.028 54 0.002705 74 s_59624, 51855, 23126, s_59625, 218 s_59626, s_59627 DPH2 s_16717, 6 958, 363, 0.028 55 0.00298 82 s_16718, 2412, 6120, s_16719, 3930, 1644 s_16720, s_16721, s_16722 DRAP1 s_16840, 4 37730, 1221, 0.028 56 0.002136 62 s_16841, 643, 31607 s_16842, s_16843 C1orf49 s_7303, 7 820, 63864, 0.028 57 0.003353 87 s_7304, 34124, 47596, s_7305, 60950, 413, s_7306, 16428 s_7307, s_7308, s_7309 ATXN2L s_4596, 2 461, 1892 0.028 58 0.000746 26 s_4597 CCT8 s_10201, 2 1836, 684 0.029 59 0.000757 28 s_10202 INA s_27443, 4 2708, 1296, 0.029 60 0.00224 64 s_27444, 502, 10303 s_27445, s_27446 SPRED1 s_53662, 3 1619, 50436, 0.029 61 0.001682 49 s_53663, 448 s_53664 FAM205A s_19797, 3 1158, 41145, 0.03 62 0.001761 52 s_19798, 1417 s_19799 ZNF679 s_64444, 4 1393, 51433, 0.03 63 0.002404 66 s_64445, 53714, 387 s_64446, s_64447 RARRES1 s_46128, 5 64493, 49693, 0.03 64 0.003121 86 s_46129, 1031, 875, s_46130, 32486 s_46131, s_46132 OXR1 s_39853, 12 635, 13208, 0.031 65 0.004951 111 s_39854, 3431, 40334, s_39855, 44056, 34602, s_39856, 40269, 15654, s_39857, 27560, 14451, s_39858, 43620, 75 s_39859, s_39860, s_39861, s_39862, s_39863, s_39864 ABCB5 s_159, 9 22148, 406, 0.031 66 0.004499 103 s_160, 716, 56705, s_161, 810, 24993, s_162, 32918, 2841, s_163, 8584 s_164, s_165, s_166, s_167 PCIF1 s_40717, 3 9090, 1441, 0.031 67 0.00186 54 s_40718, 1264 s_40719 TSPAN1 s_59367, 4 2325, 13819, 0.031 68 0.002605 71 s_59368, 864, 1297 s_59369, s_59370 GEN1 s_22609, 4 11810, 887, 0.031 69 0.002637 72 s_22610, 1299, 8422 s_22611, s_22612 EIF3D s_17807, 4 973, 21108, 0.031 70 0.00265 73 s_17808, 1274, 24555 s_17809, s_17810 CD4 s_10420, 4 1354, 17639, 0.032 71 0.002719 75 s_10421, 21819, 786 s_10422, s_10423 RASGEF1C s_46195, 3 1741, 57044, 0.032 72 0.001958 58 s_46196, 527 s_46197 RFX4 s_46955, 8 41956, 37657, 0.032 73 0.004515 104 s_46956, 844, 23401, s_46957, 35269, 57099, s_46958, 19421, 368 s_46959, s_46960, s_46961, s_46962 EP300 s_18347, 4 56572, 687, 0.032 74 0.002802 77 s_18348, 1414, 17568 s_18349, s_18350 MMS19 s_34268, 4 48047, 59609, 0.032 75 0.002818 78 s_34269, 1127, 1271 s_34270, s_34271 HEBP1 s_24995, 4 923, 46506, 0.033 76 0.002925 80 s_24996, 1368, 10469 s_24997, s_24998 DOK2 s_16643, 3 35762, 1884, 0.033 77 0.00211 60 s_16644, 306 s_16645 BRD9 s_5732, 7 827, 22740, 0.033 78 0.004695 109 s_5733, 6866, 12005, s_5734, 15293, 4165, s_5735, 858 s_5736, s_5737, s_5738 MAP1LC3A s_32578, 3 1401, 28791, 0.034 79 0.002217 63 s_32579, 1572 s_32580 GPR123 s_23666, 2 89, 2438 0.034 80 0.001072 35 s_23667 FH s_21023, 6 49396, 14069, 0.035 81 0.004382 102 s_21024, 866, 14355, s_21025, 1035, 36483 s_21026, s_21027, s_21028 NUGGC s_38328, 3 49325, 1969, 0.035 82 0.002409 67 s_38329, 470 s_38330 OR52E2 s_39294, 2 1537, 2022 0.035 83 0.001141 36 s_39295 CRNN s_13692, 6 21178, 62333, 0.036 84 0.004655 107 s_13693, 62987, 230, s_13694, 62464, 1287 s_13695, s_13696, s_13697 HDAC6 s_24909, 4 1432, 1157, 0.036 85 0.003451 88 s_24910, 37523, 5836 s_24911, s_24912 AHCYL2 s_1615, 6 1275, 536, 0.038 86 0.005333 117 s_1616, 15539, 41104, s_1617, 16156, 7154 s_1618, s_1619, s_1620 ZC3H18 s_62742, 3 885, 2013, 0.038 87 0.002841 79 s_62743, 4091 s_62744 RGS2 s_47074, 5 1366, 43591, 0.038 88 0.005052 113 s_47075, 49134, 34175, s_47076, 951 s_47077, s_47078 TMED3 s_57021, 3 2154, 20038, 0.039 89 0.00293 81 s_57022, 590 s_57023 TXNIP s_59960, 5 62111, 1181, 0.039 90 0.005299 116 s_59961, 48123, 1335, s_59962, 37778 s_59963, s_59964 MLN s_34131, 3 1893, 4200, 0.04 91 0.003008 83 s_34132, 1493 s_34133 CLEC2B s_12245, 3 52935, 1491, 0.04 92 0.003019 84 s_12246, 1898 s_12247 CASQ2 s_9253, 3 2052, 1075, 0.04 93 0.003063 85 s_9254, 53344 s_9255 GMDS s_23142, 6 27864, 18095, 0.042 94 0.006445 141 s_23143, 53905, 1284, s_23144, 13005, 944 s_23145, s_23146, s_23147 UBE2M s_60195, 2 1767, 2418 0.042 95 0.001626 46 s_60196 RNF7 s_47784, 5 1179, 21752, 0.042 96 0.006005 129 s_47785, 1461, 1846, s_47786, 56079 s_47787, s_47788 CRYGN s_13791, 3 818, 2294, 0.042 97 0.003478 89 s_13792, 7260 s_13793 NDUFA8 s_36466, 3 8398, 636, 0.043 98 0.003571 90 s_36467, 2393 s_36468 NCL s_36291, 5 13572, 1122, 0.043 99 0.006281 133 s_36292, 9807, 8470, s_36293, 1525 s_36294, s_36295 PLK4 s_42605, 5 11718, 1841, 0.043 100 0.006321 134 s_42606, 10567, 191, s_42607, 16298 s_42608, s_42609

TABLE H Output of the RIGER algorithm for the transduction replicate A375 PLX screen comparing PLX (mean of the two replicates at day 14) to DMSO control (mean of the two replicates at day 14). The weighted sum method was used to convert sgRNAs to genes. Genes are sorted by RIGER rank. # Hairpin Gene p-value Gene Hairpins Hairpins ranks NES rank p-value rank MED12 s_33340, 4 20, 18, 23, 0.00051 1 0.000002 1 s_33341, 36 s_33342, s_33343 CUL3 s_14311, 6 59797, 26, 0.0008262 2 0.000002 2 s_14312, 17, 29, s_14313, 18391, s_14314, 13751 s_14315, s_14316 NF2 s_36796, 4 71, 295, 67, 0.001589 3 0.000005 3 s_36797, 42 s_36798, s_36799 TADA1 s_55204, 4 28, 85, 0.00185 4 0.000007 4 s_55205, 2999, 379 s_55206, s_55207 TADA2B s_55211, 3 101, 107, 83 0.00213 5 0.00001 5 s_55212, s_55213 RBL1 s_46360, 3 386, 94, 245 0.004575 6 0.000041 6 s_46361, s_46362 TAF6L s_55283, 3 2738, 129, 0.006689 7 0.000085 8 s_55284, 361 s_55285 OR8S1 s_39543, 4 255, 21226, 0.008042 8 0.000157 10 s_39544, 25406, 325 s_39545, s_39546 MED23 s_33386, 2 376, 535 0.009179 9 0.000081 7 s_33387 SLC41A3 s_51930, 4 134, 50489, 0.009526 10 0.000244 14 s_51931, 441, 60192 s_51932, s_51933 CCDC101 s_9430, 3 742, 511, 0.01002 11 0.000201 11 s_9431, 283 s_9432 LCOR s_30684, 4 362, 44569, 0.01057 12 0.00031 17 s_30685, 4583, 418 s_30686, s_30687 GPR98 s_23900, 3 392, 518, 0.01074 13 0.000239 13 s_23901, 48952 s_23902 KCNA2 s_28512, 8 29441, 30891, 0.01187 14 0.000666 27 s_28513, 63671, 3716, s_28514, 48582, 37548, s_28515, 297, 194 s_28516, s_28517, s_28518, s_28519 MED15 s_33355, 4 227, 552, 0.01231 15 0.000416 18 s_33356, 711, 647 s_33357, s_33358 MT1F s_35127, 2 842, 183 0.01255 16 0.000141 9 s_35128 MYL7 s_35662, 4 135, 46125, 0.01261 17 0.000445 20 s_35663, 598, 37747 s_35664, s_35665 SLC7A11 s_52194, 5 16607, 313, 0.01288 18 0.000554 23 s_52195, 460, 5262, s_52196, 27650 s_52197, s_52198 MTRF1 s_35317, 3 17905, 41, 0.0145 19 0.000445 19 s_35318, 862 s_35319 ELF1 s_17940, 3 35910, 873, 0.01465 20 0.000454 21 s_17941, 35 s_17942 METAP1D s_33547, 4 411, 617, 0.01479 21 0.000612 25 s_33548, 35187, 34941 s_33549, s_33550 FAM160A2 s_19507, 4 48131, 49009, 0.01497 22 0.000623 26 s_19508, 459, 610 s_19509, s_19510 TAF5L s_55276, 2 57, 1089 0.0154 23 0.000207 12 s_55277 NF1 s_36794, 2 1227, 12 0.01711 24 0.000261 15 s_36795 DSEL s_16908, 2 642, 1068 0.01782 25 0.000287 16 s_16909 RAP1GAP2 s_46063, 4 740, 58091, 0.01915 26 0.000992 29 s_46064, 49142, 709 s_46065, s_46066 MPG s_34467, 6 597, 474, 0.0197 27 0.001548 41 s_34468, 37985, 7657, s_34469, 49238, 24732 s_34470, s_34471, s_34472 MED16 s_33359, 4 619, 825, 0.02023 28 0.001103 31 s_33360, 25639, 27832 s_33361, s_33362 XKR4 s_62252, 4 29846, 897, 0.02069 29 0.001163 32 s_62253, 14605, 473 s_62254, s_62255 ERP27 s_18694, 4 57819, 843, 0.02156 30 0.001269 35 s_18695, 26738, 768 s_18696, s_18697 MAB21L2 s_32293, 3 1088, 654, 0.02162 31 0.000938 28 s_32294, 49187 s_32295 ASIC5 s_3967, 5 84, 36168, 0.02172 32 0.001596 42 s_3968, 2836, 46662, s_3969, 924 s_3970, s_3971 MSMB s_35048, 5 63246, 0.02184 33 0.001613 43 s_35049, 51785, 916, s_35050, 124, 60194 s_35051, s_35052 ZNF182 s_63394, 4 856, 814, 0.02211 34 0.001328 37 s_63395, 58286, 44944 s_63396, s_63397 ZNF345 s_63726, 2 1558, 196 0.02256 35 0.000479 22 s_63727 TNFSF18 s_58159, 4 766, 19361, 0.02276 36 0.00141 39 s_58160, 905, 33444 s_58161, s_58162 NDUFAF2 s_36477, 3 1232, 0.02312 37 0.001063 30 s_36478, 22725, 494 s_36479 PDCD10 s_40840, 5 43, 3962, 0.02319 38 0.001844 49 s_40841, 1002, 5014, s_40842, 3313 s_40843, s_40844 CCNC s_10026, 5 48614, 0.02425 39 0.002022 52 s_10027, 1596, 868, s_10028, 1864, 584 s_10029, s_10030 SPRED1 s_53662, 3 950, 24805, 0.02451 40 0.001188 33 s_53663, 1164 s_53664 GDPD2 s_22566, 6 367, 60779, 0.02456 41 0.002293 57 s_22567, 819, 52875, s_22568, 24938, 6538 s_22569, s_22570, s_22571 DYRK3 s_17200, 4 9900, 22246, 0.02457 42 0.001629 44 s_17201, 1101, 455 s_17202, s_17203 MBP s_33068, 9 15442, 25428, 0.02489 43 0.002965 71 s_33069, 529, 29634, s_33070, 16368, 8819, s_33071, 36773, 478, s_33072, 52354 s_33073, s_33074, s_33075, s_33076 PARP3 s_40316, 3 506, 1352, 0.02518 44 0.001243 34 s_40317, 59418 s_40318 UBE2M s_60195, 2 491, 1665 0.02542 45 0.000595 24 s_60196 HDGF s_24936, 3 756, 1285, 0.02545 46 0.00127 36 s_24937, 5163 s_24938 KCNC2 s_28558, 7 42492, 6191, 0.02554 47 0.002731 66 s_28559, 648, 54771, s_28560, 50213, 652, s_28561, 22159 s_28562, s_28563, s_28564 GALNS s_22109, 4 999, 8504, 0.02604 48 0.00184 47 s_22110, 52589, 986 s_22111, s_22112 METTL21B s_33609, 4 46303, 472, 0.02605 49 0.001842 48 s_33610, 1171, 29308 s_33611, s_33612 BTBD17 s_5890, 3 1185, 0.02641 50 0.001371 38 s_5891, 64382, 1200 s_5892 HSD11B1 s_26144, 5 1048, 391, 0.02689 51 0.002482 61 s_26145, 7446, 21804, s_26146, 42773 s_26147, s_26148 LGR5 s_30925, 4 1394, 241, 0.02892 52 0.002269 56 s_30926, 38237, 49566 s_30927, s_30928 BUB1B s_5999, 4 30283, 1179, 0.02924 53 0.0023 58 s_6000, 47822, 935 s_6001, s_6002 MRFAP1L1 s_34603, 3 18516, 421, 0.02926 54 0.00168 45 s_34604, 1627 s_34605 CCDC83 s_9835, 4 1148, 21192, 0.02932 55 0.002316 59 s_9836, 1041, 54459 s_9837, s_9838 DRAP1 s_16840, 4 33445, 508, 0.02937 56 0.002321 60 s_16841, 1328, 44015 s_16842, s_16843 RELT s_46777, 3 187, 61852, 0.02984 57 0.001756 46 s_46778, 1740 s_46779 RANBP9 s_46039, 3 1837, 11418, 0.0307 58 0.001849 50 s_46040, 52 s_46041 HMMR s_25651, 4 1502, 48474, 0.03099 59 0.002589 64 s_25652, 27570, 234 s_25653, s_25654 MALSU1 s_32462, 3 1575, 5215, 0.03115 60 0.001886 51 s_32463, 920 s_32464 TACC1 s_55171, 6 4921, 24086, 0.03181 61 0.003733 94 s_55172, 6177, 328, s_55173, 10098, 1110 s_55174, s_55175, s_55176 HOXC13 s_25901, 4 9058, 894, 0.03205 62 0.00277 67 s_25902, 1336, 22970 s_25903, s_25904 EAPP s_17273, 4 1388, 21167, 0.03259 63 0.002875 68 s_17274, 820, 26512 s_17275, s_17276 C1QA s_6997, 6 26254, 946, 0.03263 64 0.003918 99 s_6998, 914, 57738, s_6999, 2934, 961 s_7000, s_7001, s_7002 SELRC1 s_49728, 3 1215, 6860, 0.03276 65 0.00209 53 s_49729, 1574 s_49730 B3GALNT2 s_4738, 6 827, 29762, 0.03279 66 0.003962 101 s_4739, 38965, 31290, s_4740, 23785, 981 s_4741, s_4742, s_4743 RBM15B s_46395, 3 893, 1695, 0.03299 67 0.002127 54 s_46396, 44505 s_46397 PDE12 s_40901, 6 2381, 1262, 0.03326 68 0.004098 104 s_40902, 58589, 2108, s_40903, 38, 10016 s_40904, s_40905, s_40906 PAFAH2 s_40041, 6 5602, 61209, 0.03339 69 0.004132 106 s_40042, 1155, 63735, s_40043, 375, 37029 s_40044, s_40045, s_40046 LAMA3 s_30412, 8 9450, 1177, 0.03369 70 0.005071 132 s_30413, 17134, 27544, s_30414, 874, 456, s_30415, 38308, 45063 s_30416, s_30417, s_30418, s_30419 TDRD5 s_55980, 6 1131, 41843, 0.03397 71 0.004252 108 s_55981, 44717, 513, s_55982, 54260, 50377 s_55983, s_55984, s_55985 MBNL2 s_33046, 4 60513, 1365, 0.03435 72 0.003193 76 s_33047, 1158, 40330 s_33048, s_33049 ADI1 s_1254, 6 1267, 209, 0.03487 73 0.004464 111 s_1255, 12112, 3449, s_1256, 25692, 52308 s_1257, s_1258, s_1259 MED19 s_33371, 4 306, 12467, 0.03523 74 0.003361 81 s_33372, 2378, 1694 s_33373, s_33374 PRKRA s_44162, 5 47085, 863, 0.03524 75 0.004253 109 s_44163, 19810, 1257, s_44164, 23209 s_44165, s_44166 ATP1B4 s_4304, 4 1486, 31149, 0.03532 76 0.003379 83 s_4305, 944, 43483 s_4306, s_4307 PRR7 s_44424, 4 904, 38806, 0.03545 77 0.003414 84 s_44425, 59763, 1506 s_44426, s_44427 GBP2 s_22365, 6 1003, 60810, 0.03557 78 0.004654 116 s_22366, 58109, 1029, s_22367, 43443, 48442 s_22368, s_22369, s_22370 KCTD15 s_28890, 4 23114, 8725, 0.03616 79 0.003546 87 s_28891, 1747, 290 s_28892, s_28893 MAPKAPK3 s_32778, 4 1795, 169, 0.03631 80 0.003576 89 s_32779, 21907, 29592 s_32780, s_32781 MRPS12 s_34814, 3 1726, 1417, 0.0364 81 0.002585 63 s_34815, 15155 s_34816 TNR s_58261, 6 1368, 52097, 0.03661 82 0.004941 127 s_58262, 29987, 60673, s_58263, 37039, 106 s_58264, s_58265, s_58266 PET117 s_41313, 3 1789, 1416, 0.03666 83 0.002611 65 s_41314, 1742 s_41315 SRM s_53860, 5 1466, 5441, 0.03672 84 0.004589 114 s_53861, 2247, 3169, s_53862, 430 s_53863, s_53864 INO80E s_27530, 4 46304, 1464, 0.03707 85 0.003727 93 s_27531, 1278, 16053 s_27532, s_27533 ZSWIM6 s_64963, 4 25840, 1465, 0.0372 86 0.003755 95 s_64964, 19204, 1294 s_64965, s_64966 SLC4A3 s_52020, 6 29005, 52591, 0.03732 87 0.005147 134 s_52021, 64538, 39136, s_52022, 1319, 334 s_52023, s_52024, s_52025 CDKL4 s_10939, 4 63413, 1274, 0.03795 88 0.003903 98 s_10940, 36650, 1510 s_10941, s_10942 EED s_17448, 4 1999, 352, 0.03863 89 0.004041 103 s_17449, 1852, 22596 s_17450, s_17451 MRPL17 s_34661, 3 2009, 1162, 0.03885 90 0.002918 69 s_34662, 1959 s_34663 ANGEL2 s_2338, 5 28245, 840, 0.03886 91 0.005154 135 s_2339, 1423, 56505, s_2340, 62188 s_2341, s_2342 PLK1 s_42592, 4 18870, 1327, 0.03896 92 0.00412 105 s_42593, 15990, 1544 s_42594, s_42595 CARS2 s_9155, 3 1198, 1989, 0.03954 93 0.003005 72 s_9156, 11196 s_9157 PODN s_42919, 6 49093, 58125, 0.03971 94 0.005858 150 s_42920, 330, 36756, s_42921, 41658, 1412 s_42922, s_42923, s_42924 AMPD2 s_2260, 6 672, 1977, 0.03997 95 0.005936 151 s_2261, 27046, 41151, s_2262, 34556, 1308 s_2263, s_2264, s_2265 TRIM67 s_59007, 2 2416, 1455 0.04032 96 0.001521 40 s_59008 ACOX1 s_673, 3 618, 2238, 0.04046 97 0.003153 74 s_674, 44076 s_675 PRPF4B s_44329, 3 17853, 1143, 0.04046 98 0.003153 75 s_44330, 2063 s_44331 TCEB2 s_55778, 4 3561, 1732, 0.04073 99 0.004475 112 s_55779, 1896, 1034 s_55780, s_55781 VAX1 s_61156, 5 61659, 1770, 0.04079 100 0.005648 147 s_61157, 53, 22962, s_61158, 60237 s_61159, s_61160

A similar screen to identify PLX drug resistance in A375 cells was previously conducted using a pooled library of 90,000 shRNAs. To compare the efficacy and reliability of genome-scale shRNA screen with GeCKO, Applicants used several methods to evaluate the degree of consistency among the multiple sgRNAs or shRNAs for the top candidate genes. First, Applicants calculated the aggregate p value distribution for the top 100 hits using either RIGER (FIG. 28A) or RSA (FIG. 37) scoring. Lower p values for the GeCKO versus shRNA screen indicate better scoring consistency among sgRNAs. Second, for the top 10 RIGER hits, 78±27% of the sgRNAs targeting each gene ranked among the top 5% of enriched sgRNAs, whereas 20±12% of shRNAs targeting each gene ranked among the top 5% of enriched shRNAs (FIG. 28B).

Applicants validated top ranking genes from the GeCKO screen individually using 3-5 sgRNAs (FIGS. 28C-E, 38, 39). For NF2, Applicants found that 4/5 sgRNAs resulted in >98% allele modification 7 days post-transduction, and all 5 sgRNAs showed >99% allele modification 14 days post-transduction (FIG. 28C). Applicants compared sgRNA and shRNA-mediated protein depletion and PLX resistance using Western blot (FIG. 28D) and cell growth assays (FIG. 28E). Interestingly, while all five sgRNAs conferred resistance to PLX, only the best shRNA achieved sufficient knockdown to increase PLX resistance (FIG. 28E), suggesting that even low levels of NF2 are sufficient to retain sensitivity to PLX. Addtionally, sgRNAs targeting NF1, MED12, CUL3, TADA1, and TADA2B led to a decrease in protein expression and increased resistance to PLX (FIGS. 38, 39). Deep sequencing confirmed a high rate of mutagenesis at targeted loci (FIGS. 40, 41), with a small subset of off-target sites exhibiting indels (FIGS. 42-44), which may be alleviated using an offset nicking approach that was shown to reduce off-target modifications.

GeCKO screening provides a complementary method to RNAi for systematic perturbation of gene function through generation of loss of function alleles. This can be useful in cases where incomplete knockdown retains gene function. The ability to achieve targeted genome modifications on a large scale using custom Cas9:sgRNA libraries presents unique opportunities to probe a broad range of coding and non-coding genomic elements.

GeCKO screening is carried out in three steps: Step 1—Library Design. Constitutive exons near the 5′ end of transcripts are identified using Illumina Human BodyMap 2.0 and NCBI CCDS datasets. sgRNAs were ranked by an off-target score using a metric that includes the number of off-targets in the genome and the type of mutations (distance from protospacer-adjacent motif and clustering of mismatches) and those with lowest off-target scores were selected. This resulted in a library in which most genes have an average of 3 or 4 sgRNAs. Step 2—Viral vector generation. The sgRNA library was synthesized using array synthesis and cloned as a pool into the lentiCRISPR transfer plasmid for virus production. Viral vectors were produced in HEK293T cells and concentrated to increase viral titer. Cells of interest were infected at a low MOI (0.3) to ensure that most cells receive only 1 viral construct with high probability. Step 3—Readout. 24 hours after transduction, cells were selected with puromycin so that only cells transduced with a lentiCRISPR construct are preserved. At this point the cells can be used to carry out either positive or negative selection screens.

Screening timeline considerations: After infection, cells are selected with puromycin. For most cell types, 0.5-2 ug/ml puromycin works well, although the minimum dose that kills all cells without any viral transduction should be determined in advance and the minimum concentration should be used for selection. Usually, only 2-3 days of puromycin selection is needed to select for cells with viral integration and expression but a longer period of selection has the added benefit of allowing for enough time for genome modification by Cas9. As shown in the deep sequencing of the individual target (array) validations from the PLX resistance screen gene hits, genome modification increases over time. For most targets, genome modification was nearly complete after only 7 days. Some lentiCRISPRs had lower modification that increased by 14 days post-transduction (for example, NF sg4 in FIG. 42, NF2 sg5 in FIG. 43). As expected, for some sgRNAs, off-target modification also increases with time, albeit by a smaller amount (for example, NF2 sg4 in FIG. 42, MED12 sg2 in FIG. 43). In general, it is advisable to keep puromycin selection (and Cas9 expression since they are co-expressed) for at least 7 days post-transduction and possibly longer depending on the needs of the particular experiment.

Identification of gene candidates: Before any experiment, it is important to determine the distribution of sgRNAs before any selection pressure has been applied. This baseline sgRNA distribution will be used to infer either depletion or enrichment of specific sgRNA species. For both positive and negative selection screens, hits are identified by comparing the distribution of sgRNAs after selection with the baseline sgRNA distribution. Candidate genes are identified by searching for sgRNAs whose frequency has either significantly reduced or increased after selection for negative and positive screens respectively.

Using multiple sgRNAs to target the same gene, and transduction replicates are the main experimental features that enable discrimination between true and false positive hits. The reason is that each screen will have some background rate, meaning that with some probability an sgRNA can be enriched (or depleted) despite having no effect on the studied phenotype. The required number of unique sgRNAs for the same genes should be determined by the background rate of the screen and the overall efficacy of sgRNAs. As increasing sgRNA numbers per gene comes with a cost of increasing library complexity, additional infection replicates can compensate for it as long as there is a minimal number of sgRNAs that can effectively mediate gene targeting. Finally, ranking of the top hits requires the conversion of sgRNA scores into gene rankings. A simple method is to rank gene hits according to the mean or median of all sgRNAs for each respective gene. Applicants recommend combining this simple method with other analysis such as RIGER and RSA.

GeCKO versus shRNA screening: GeCKO screening operates through a fundamentally different mechanism than shRNA based screening. Whereas shRNAs reduce protein expression by targeting the mRNA, GeCKO achieves protein knockdown via frameshift mutations introduced into the genomic coding region. GeCKO-mediated frameshift mutations are achieved through targeted DNA double strand breaks (DSB) and subsequent mutagenic repair via the non-homologous end joining (NHEJ) pathway, which produces indels at the site of DSB. The indel being introduced into the DSB is random (FIG. 44), with some indels leading to frameshift mutations that cause premature termination of the transgene. Other indels with lengths that are multiples of three will not result in the frameshift of the candidate genes. In this scenario, the gene product might still be functional. In contrast, shRNA knockdown can generate a spectrum of expression levels of the target genes. Therefore GeCKO screening can provide potential advantages over shRNA, where the population of cells that has been homozygously knocked out can provide more screening sensitivity especially when probing gene products that can function normally even at significantly reduced concentrations.

Vemurafenib (PLX) resistance mechanisms: The protein kinase BRAF, a key regulator of the MAPK signaling cascade, is mutated in more than half of malignant melanomas and in several other types of cancer, such as thyroid, colorectal, lung, and hairy cell leukemia. The V600E mutant form of BRAF is a common gain of function mutation that allows BRAF to remain in a constitutively active state and phosphorylate MEK without forming a phosphorylated BRAF dimer. Vemurafenib (PLX) is a FDA-approved, ATP-competitive RAF inhibitor that displays higher binding affinity for V600E mutant BRAF over other RAF isoforms, including wild-type BRAF. Over 50% of melanoma patients with mutated BRAF treated with PLX display tumor reduction, but the effect is short-lived and resistance develops in a majority of cases. By applying the GeCKO library to A375 cells (which are homozygous for the BRAF V600E mutation), Applicants identified several genes whose loss resulted in resistance to PLX.

In the PLX screen, Applicants identified and validated NF2, NF1, MED12, CUL3, TADA1, and TADA2B as genes whose loss results in PLX resistance. Loss of NF1 and MED12 were previously identified resistance mechanisms from two separate, large-scale RNAi screens. MED12, a member of the Mediator transcription complex, is a negative regulator of TGF-βR and its loss results in activation of TGF-βR signaling and MEK/ERK. NF1 is a negative regulator of NRAS activity and its loss phenocopies activating NRAS mutations, an established PLX resistance mechanism.

Although they have similar names, NF1 and NF2 are tumor suppressors that function via distinct pathways. NF2 (or Merlin, Moesin-Ezrin-Radixin-Like Protein) is a tumor suppressor gene that encodes a cytoskeletal protein. Loss of NF2 leads to constitutive mTOR activation and cell proliferation by a MEK/ERK-independent mechanism and involves the Hippo signaling pathway. Mutation and copy number variation of the E3 ligase CUL3 has been described in lung squamous cell carcinomas and renal cell carcinomas. Quantitative proteomics in T24T bladder cancer cells found that silencing of CUL3 restored the expression of cytoskeleton proteins that are underexpressed in T24T, such as moesin and erzin. This suggests a possible interaction between CUL3 and NF2/merlin, a similar cytoskeletal protein to those ubiquitinated by CUL3.

TADA1 and TADA2B are chromatin-modifying enzymes involved in transcription and are members of the multiprotein STAGA (SPT3-TAF9-GCN5-acetylase) complex. The STAGA complex recruits Mediator complex proteins (such as MED12) to the oncoprotein c-Myc to activate proliferation. Applicants noted that CCDC101 had a high RIGER rank in both infection replicates (see Table I) and is also a subunit of the STAGA complex and thus may lead to PLX resistance through a similar mechanism as TADA1 and TADA2B. Since many of the gene hits from the PLX screen interact with each other and are involved in established cell proliferation pathways, therapeutics targeted to these pathways could be combined with BRAF inhibition to achieve better clinical outcomes in melanoma and other cancers.

Other applications of GeCKO screening: In addition to facilitating loss-of-function gene screening, GeCKO and similar Cas9-sgRNA libraries can be customized to carry out a variety of genome-scale perturbations to study the effect of non-coding elements, transcriptional changes, and epigenetic modulations. In this library, Applicants target the constitutive exons near the 5′ end of genes for loss-of-function but sgRNAs can also be targeted to promoters, enhancers, intronic, and intergenic regions. Screens targeting non-coding regions or a mix of coding and non-coding regions can elucidate how these different elements contribute to gene expression and biological function. As Applicants have recently shown, Cas9 with mutated catalytic residues can be fused to a transcriptional activation domain such as VP16 or repressor domain such as SID4X or KRAB to create a Cas9 transcriptional modulator without any nuclease activity. By replacing the Cas9 in the lentiCRISPR plasmid with a null-nuclease version (e.g. with D10A and H840A mutations), libraries of sgRNAs for activation can be used to investigate how activation of different transcripts or different splice variants contribute to a screen phenotype. A null-nuclease Cas9 could also be fused with different effector domains capable of modifying the epigenetic state at a particular locus. Previous work from Applicants and others has demonstrated transcriptional changes using zinc-finger proteins and transcriptional activator like effectors (TALEs) fused to histone (de)acetylases, histone (de)methylases, DNA (de)methylases and other epigenetic modifiers. The easy programmability of Cas9 DNA binding using sgRNAs that can be array synthesized en masse opens up many new possibilities for genome-scale screens.

TABLE I Comparison of the top 20 hits between the two A375 PLX infection replicate screens by RIGER rank. RNAi gene enrichment ranking (RIGER) uses a two-sample weighted likelihood ratio test to measure the support for a gene using the enrichment of the sgRNAs (or shRNAs) for each gene. 1st infection 2nd infection Gene RIGER RIGER Gene RIGER RIGER symbol rank p-value symbol rank p-value NF2  1 0.000004 MED12  1 0.000002 MED12  2 0.000004 CUL3  2 0.000002 CUL3  3 0.000006 NF2  3 0.000005 CLDN10  4 0.000005 TADA1  4 0.000007 NF1  5 0.000001 TADA2B  5 0.00001  TADA1  6 0.000035 RBL1  6 0.000041 TADA2B  7 0.000046 TAF6L  7 0.000085 SPECC1  8 0.000146 OR8S1  8 0.000157 CCDC101  9 0.000082 MED23  9 0.000081 ALG3 10 0.000118 SLC41A3 10 0.000244 P4HB 11 0.000189 CCDC101 11 0.000201 EED 12 0.000313 LCOR 12 0.00031  TAF6L 13 0.000234 GPR98 13 0.000239 MED15 14 0.000382 KCNA2 14 0.000666 NPPC 15 0.000575 MED15 15 0.000416 TAF5L 16 0.000141 MT1F 16 0.000141 PGD 17 0.000349 MYL7 17 0.000445 LGALS4 18 0.00051  SLC7A11 18 0.000554 TAOK1 19 0.000429 MTRF1 19 0.000445 CD320 20 0.000824 ELF1 20 0.000454 appear in the top 20 of the other replicate infection appears in the top 100 of the other replicate infection (in bold)

TABLE J Comparison of the top 20 hits between the two A375 PLX infection replicate screens by RSA rank. Redundant siRNA activity (RSA) uses an enrichment cutoff and hypergeometric test to measure the support for a gene using the enrichment of the sgRNAs (or shRNAs) for each gene. 1st infection 2nd infection Gene RSA RSA log Gene RSA RSA log symbol rank p value symbol rank p value MED12  1 −12.467 MED12  1 −11.954 NF2  2 −9.147 NF2  2 −8.766 CUL3  3 −8.578 CUL3  3 −8.174 MED15  4 −7.684 TADA2B  4 −6.512 TADA2B  5 −7.418 CCDC101  5 −6.319 RBL1  6 −6.316 DPH2  6 −6.141 TADA1  7 −5.815 MED15  7 −5.609 CCNC  8 −5.483 NF1  8 −5.418 CCDC101  9 −5.313 CLDN10  9 −5.174 PDCD10 10 −5.278 PGD 10 −4.944 NOTCH2NL 11 −4.988 TADA1 11 −4.909 PCLO 12 −4.971 ZEB2 12 −4.892 PPP1R8 13 −4.947 CCNC 13 −4.697 C1QA 14 −4.667 TAF6L 14 −4.402 DR1 15 −4.311 SMARCB1 15 −4.371 KCTD10 16 −4.284 BCL2L12 16 −4.228 PDE12 17 −4.236 PDCD10 17 −4.16 SLC25A17 18 −4.209 GADD45GIP1 18 −4.107 BRD9 19 −4.206 ZNF592 19 −4.037 PET117 20 −4.168 ACTA2 20 −4.033 appear in the 20 top of other replicate infection appears in the 100 top of other replicate infection (in bold)

TABLE K Cas9-sgRNA array screening constructs used. Names and targeting sequence for all Cas9-sgRNA constructs used for validation in A375 screen. Cas9-sgRNAs (SEQ ID NOs: 24-51, respectively, in order of appearance) with names in italics are contained in the GeCKO library. Name sg RNA 20 bp sequence NF2_sg1 AAACATCTCGTACAGTGACA NF2_sg2 ATTCCACGGGAAGGAGATCT NF2_sg3 CCTGGCTTCTTACGCCGTCC NF2_sg4 GTACTGCAGTCCAAAGAACC NF2_sg5 CACAGTGGCCTGGCTCAAAA MED12_sg1 AGGATTGAAGCTGACGTTCT MED12_sg2 CGTCAGCTTCAATCCTGCCA MED12_sg3 CTCAGAGATTGCTGCATAGT MED12_sg4 ACAGGTCATCTTAATGAGCC MED12_sg5 GGGGCTGTGGTTCCACGATA NF1_sg1 GTTGTGCTCAGTACTGACTT NF1_sg2 ACACTGGAAAAATGTCTTGC NF1_sg3 AGTCAGTACTGAGCACAACA CUL3_sg1 CTTACCTGGATATAGTCAAC CUL3_sg2 GAATCCTGTTGACTATATCC CUL3_sg3 GACCTAAAATCATTAACATC CUL3_sg4 TGCCAGATGTTAATGATTTT CUL3_sg5 TTATTTAGTCGTGTGCCAAA TADA1_sg1 ACTGGGCTAACCTAAAGCTG TADA1_sg2 TCTGCTTGAACCACAGCTTT TADA1_sg3 GGAGGAAATCATTGTGAGAA TADA1_sg4 TCTTTAGTGCAATCAGAATC TADA2B_sg1 ACGGCGGGCGCTTCACGCTC TADA2B_sg2 GCCATCGAGCAGTTCGGCTT TADA2B_sg3 GCACCTTCTCGCGATCTGAC TADA2B_sg4 GCTCCTGTCAGATCGCGAGA Control_sg1 (EGFP_sg5) GAAGTTCGAGGGCGACACCC Control_sg2 (EGFP_sg6) GGTGAACCGCATCGAGCTGA

TABLE L shRNA array screening constructs (SEQ ID NOs: 52-66, respectively, in order of appearance) used. Names and The RNAi Consortium (TRC) identification numbers for all shRNA constructs used for validation in A375 screen. Name TRC ID Targeting Sequence NF2_sh1 TRCN0000010397 GAAGCAACCCAAGACGTTCAC NF2_sh2 TRCN0000018338 TAGTTCTCTGACCTGAGTCTT NF2_sh3 TRCN0000039974 GCTCTGGATATTCTGCACAAT NF2_sh4 TRCN0000039975 GCTTCGTGTTAATAAGCTGAT MED12_sh1 TRCN0000018574 GCAGCATTATTGCAGAGAAAT MED12_sh2 TRCN0000018575 GCTGTTCTCAAGGCTGTGTTT MED12_sh3 TRCN0000018576 CGGGTACTTCATACTTTGGAA MED12_sh4 TRCN0000018578 GCAGAGAAATTACGTTGTAAT NF1_sh1 TRCN0000039714 GCCAACCTTAACCTTTCTAAT NF1_sh2 TRCN0000039715 CCTCACAACAACCAACACTTT NF1_sh3 TRCN0000039716 CCTGACACTTACAACAGTCAA NF1_sh4 TRCN0000039717 GCTGGCAGTTTCAAACGTAAT TADA2B_sh1 TRCN0000237951 CGTGACTGTGAAGACTATTAT TADA2B_sh2 TRCN0000237949 ATGATTACGAGATCGAGTATG TADA2B_sh3 TRCN0000237950 ACATCGCCCGTGACTACAATC NullT_1 TRCN0000208001 n/a NullT_2 TRCN0000231782 n/a

GeCKO library design: A genome-scale sgRNA library was constructed as follows: First, early constitutive exons were identified for all coding genes. Then, sgRNAs to target these early constitutive exons were selected by choosing sgRNAs that were predicted to have minimal off-target activity.

To identify constitutive exons, RNA sequencing data from the Illumina Human Body Map 2.0 (GEO accession number: GSE30611) was mapped to the reference human genome (hg19) using TopHat v1.0.14 and transcripts were reconstructed with Cufflinks v1.0.2, as previously described in Merkin J. et al. Science 338, 1593 (Dec. 21, 2012). Exons expressed across all tissues in the Illumina dataset were chosen as constitutive exons for sgRNA targeting. In addition, for each gene, the first and last exons were excluded along with any exon that contained an alternative splicing site.

For the constitutive exons, genomic sequences were retrieved from the NCBI Consensus CoDing Sequence database (available at the website of ncbi.nlm.nih.gov/CCDS/). For each CCDS entry, the two earliest constitutive exons were chosen as candidate exons for library design. For genes without RNA sequencing data or where no exons qualified as constitutive, exons 2 and 3 were included as candidate exons for library design.

Next, for each candidate exon, all possible S. pyogenes Cas9 sgRNA sequences of the form (N)₂₀NGG were listed as candidate targets. Each 20mer candidate sgRNA was mapped to a precompiled index containing all 20mer sequences in the human genome followed by either NGG or NAG. This mapping was done using Bowtie short read aligner, allowing up to 3 base mismatches.

The following heuristic was used to rank sgRNAs for each exon based on the characterized sequence specificity of Cas9 nuclease. First, any sgRNAs with other targets in the genome that match exactly or differ by only 1 base are discarded. For the remaining sgRNAs, Applicants calculated the following off target score:

${OS} = {\sum\limits_{{off}\mspace{14mu} {targets}}{\left( {{sum}\mspace{14mu} \min \mspace{14mu} {location}} \right)\left( \frac{D\left( \min \right)}{D\left( \max \right)} \right)}}$

sum mm location=sum of the mismatch locations from 3′ to 5′. The PAM (NGG) proximal base is 1 and the PAM distal base is 20. D(mm)=distance in bp between mismatch locations. D(max)=maximal possible distance between 2 or 3 mismatches.

When mismatches are clustered more closely together, the cutting efficiency of Cas9 is significantly lower. Therefore, in the OS, the location of mismatches is weighted by their distances from each other. For each gene, the best (lowest OS) sgRNAs were chosen with the constraint that no sgRNAs have a 05′5400. This resulted in a library of 64,751 unique sgRNAs targeting 18,080 coding genes with an average of 3-4 sgRNAs per gene. For all sgRNAs, an extra 5′ G was added to improve U6 transcription.

Array oligo synthesis and pooled library cloning: DNA oligonucleotide library synthesis was performed on a programmable microarray using a B3 Synthesizer (CustomArray) and SAFC Proligo reagents (Sigma), as recommended by the manufacturer. The synthesis products were cleaved from the microarray and deprotected by overnight incubation in 28-30% ammonium hydroxide at 65° C., dried, resuspended in TE buffer and then purified using a QlAquick spin column (Qiagen). Full-length oligonucleotides (74 nt) were amplified by PCR using Phusion HS Flex (NEB) and size-selected using a 2% agarose E-Gel EX (Life Technologies, Qiagen).

ArrayF (SEQ ID NO: 67) TAACTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGAC GAAACACCG ArrayR (SEQ ID NO: 68) ACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCT AGCTCTAAAAC

The lentiCRISPR vector was digested with BsmBI (Fermentas) and treated with alkaline phosphatase (Fermentas) at 37° C. for 2 hours and gel-purified on a 1% E-Gel EX (Life Technologies, Qiagen). A 20 ul Gibson ligation reaction (NEB) was performed using 10 ng of the gel-purified inserts and 25 ng of the vector. From the ligation, 0.5 ul of the reaction was transformed into 25 ul of electrocompetent cells (Lucigen) according to the manufacturer's protocol using a GenePulser (BioRad). To ensure no loss of representation, 36 parallel transformations were performed using the same ligation reaction and plated onto 245 mm×245 mm plates (Corning) with carbenicillin selection (50 ug/ml), which yielded 166×library coverage. Colonies were scraped off plates and combined before plasmid DNA extraction using Endotoxin-Free Plasmid Maxiprep (Qiagen).

Lentivirus production and purification: To produce lentivirus, twelve T-225 flasks of HEK293T cells (Broad RNAi Platform) were seeded at ˜40% confluence the day before transfection in D10 media (DMEM supplemented with 10% fetal bovine serum). One hour prior to transfection, media was removed and 13 mL of pre-warmed reduced serum OptiMEM media (Life Technologies) was added to each flask. Transfection was performed using Lipofectamine 2000 and Plus reagent (Life Technologies). For each flask, 200 ul of Plus reagent was diluted in 4 ml OptiMEM (Life Technologies) with 20 ug of lentiCRISPR plasmid library, 10 ug of pVSVg, and 15 ug of psPAX2 (Addgene). 100 ul of Lipofectamine 2000 was diluted in 4 ml OptiMEM and, after 5 min, it was added to the mixture of DNA and Plus reagent. The complete mixture was incubated for 20 min before being added to cells. After 6 h, the media was changed to 30 ml D10 supplemented with 1% BSA (Sigma).

After 60 h, the media was removed and centrifuged at 3,000 rpm at 4° C. for 10 min to pellet cell debris. The supernatant was filtered through a 0.45 um low protein binding membrane (Millipore Steriflip HV/PVDF). To achieve 300× concentration of the GeCKO pooled library, the virus was ultracentrifuged (Sorvall) at 24,000 rpm for 2 h at 4° C. and then resuspended overnight at 4° C. in D10 supplemented with 1% BSA. Aliquots were stored at −80° C.

Cell transduction using the GeCKO library: Cells were transduced with the GeCKO library via spinfection. To find optimal virus volumes for achieving an MOI of 0.3-0.5, each new cell type and new virus lots were tested by spinfecting 3×10⁶ cells with several different volumes of virus. Briefly, 3×10⁶ cells per well were plated into a 12 well plate in the appropriate standard media for the cell type (see below) supplemented with 8 ug/ml polybrene (Sigma). For A375 cells (ATCC), standard media was R10: RPMI 1640 supplemented with 10% FBS. For HUES62 (Harvard Stem Cell Institute iPS Core Facility), standard media consists of mTeSR1 (STEMCELL Technologies) supplemented with 1× Normocin (InvivoGen). Each well received a different titrated virus amount (usually between 5 and 50 ul) along with a no-transduction control. The 12-well plate was centrifuged at 2,000 rpm for 2 h at 37° C. After the spin, media was aspirated and fresh media (without polybrene) was added.

Cells were incubated overnight and then enzymatically detached using trypsin (Corning) for A375 and Accutase (STEMCELL) for HUES62. Cells were counted and each well was split into duplicate wells. One replicate received 0.5 ug/mL puromycin (Sigma) for HUES62 cells or 1 ug/ml puromycin for A375 cells. After 3 days (or as soon as no surviving cells remained in the no-transduction control under puromycin selection), cells were counted to calculate a percent transduction. Percent transduction is calculated as cell count from the replicate with puromycin divided by cell count from the replicate without puromycin multiplied by 100. The virus volume yielding a MOI closest to 0.4 was chosen for large-scale screening.

Large-scale spinfection of 5×10⁷ to 1×10⁸ A375 or HUES62 cells was carried out in the same way as described above using 12-well plates with 3×10⁶ cells per well. Wells were pooled together into larger flasks on the day after spinfection.

HUES62 depletion screen: 6×10⁷ HUES62 human embryonic stem (hES) cells were transduced as described above. 30 uL of the concentrated GECKO library was applied to each well containing 3×10⁶ cells, resulting in an transduction efficiency of 30% (approximately 270 cells per lentiCRISPR construct). Puromycin (0.5 ug/mL) was added to the cells 24 hours post transduction and maintained for 7 days. On day 7, cells were split into replicate flasks with a minimum of 2×10⁷ cells per replicate and cultured for an additional 14 days before genomic DNA extraction and analysis. During the screen, hES cells were fed daily with mTeSR1.

A375 PLX-4032 resistance screen: 8×10⁷ A375 cells were transduced as described above with 2×10⁶ cells plated per transduction well. 10 uL of the concentrated GECKO library was applied to each well containing 2×10⁶ cells, attaining a transduction efficiency of 30% (approximately 370 cells per lentiCRISPR construct or in aspects of the invention, this may be approximately 400 cells per lentiCRISPR construct). Puromycin (1 ug/mL) was added to the cells 24 hours post transduction and maintained for 7 days. On day 7, cells were split into drug conditions in duplicate with a minimum of 2.6×10⁷ cells per replicate and an additional 3×10⁷ cells were frozen down for genomic DNA analysis. Two replicates were cultured in R10 supplemented with 2 uM PLX4032 (Selleckchem) and two replicates were cultured in R10 supplemented with an equal volume DMSO (Sigma Aldrich). Replicates were either passaged or fresh media was added every 2-3 days. Cell pellets with a minimum of 3×10⁷ cells were taken at 7 days after drug addition and 14 days after drug addition at which point the screen was terminated.

Genomic DNA sequencing: Frozen cell pellets were thawed and genomic DNA was extracted with a Blood & Cell Culture Midi kit (Qiagen). PCR was performed in two steps: For the first PCR, the amount of input genomic DNA (gDNA) for each sample was calculated in order to achieve 300X coverage over the GECKO library, which resulted in 130 ug DNA per sample (assuming 6.6 ug of gDNA for 10⁶ cells). For each sample, Applicants performed 13 separate 100 ul reactions with 10 ug genomic DNA in each reaction using Herculase II Fusion DNA Polymerase (Agilent) and then combined the resulting amplicons. Primers sequences (SEQ ID NOs: 69 and 70, respectively, in order of appearance) to amplify lentiCRISPR sgRNAs for the first PCR are:

F1 AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCG R1 CTTTAGTTTGTATGTCTGTTGCTATTATGTCTACTATTCTTTCC

A second PCR was performed to attach Illumina adaptors and to barcode samples. The second PCR was done in a 100 ul reaction volume using 5u1 of the product (preferably the pooled product) from the first PCR. Primers for the second PCR include both a variable length sequence to increase library complexity and an 8 bp barcode for multiplexing of different biological samples:

F2 (SEQ ID NO: 71) AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTT CCGATCT (1-9 bp variable length sequence)(8 bp barcode)tcttgtggaaaggacgaaacaccg R2 (SEQ ID NO: 72) CAAGCAGAAGACGGCATACGAGATGTGACTGGAGTTCAGACGTGTGCTCTT CCGATCT tctactattctttcccctgcactgt

Resulting amplicons from the second PCR were gel extracted, quantified, mixed and sequenced using a HiSeq 2500 (Illumina). Amplification was carried out with 18 cycles for the first PCR and 24 cycles for the second PCR.

Data processing and initial analysis: Raw FASTQ files were demultiplexed using the FASTX-Toolkit (available at the website of hannonlab. cshl.edu/fastx toolkit/) and processed to contain only the unique sgRNA sequence. To align the processed reads to the library, the designed sgRNA sequences from the library were assembled into a Burrows-Wheeler index using the Bowtie build-index function. Reads were then aligned to the index using the Bowtie aligner. After alignment, the number of uniquely aligned reads for each library sequence was calculated.

The numbers of reads for each unique sgRNA for a given sample were normalized as follows:

${{normalized}\mspace{14mu} {reads}\mspace{14mu} {per}\mspace{14mu} {sgRNA}} = {\frac{{READS}\mspace{14mu} {PER}\mspace{14mu} {sgRNA}}{{total}\mspace{14mu} {reads}\mspace{14mu} {for}\mspace{14mu} {all}\mspace{14mu} {sgRNAs}\mspace{14mu} {in}\mspace{14mu} {sample}} \times 10^{6}}$

Array lentiCRISPR array screen: Individual lentiCRISPRs from the GECKO pool were produced as above except that viral supernatants were not concentrated by ultracentrifugation. For each lentiCRISPR, 5×10⁵ A375 cells were infected via spinfection at 2,000 rpm for 2 h at 37° C. in R10 supplemented with Bug/ml polybrene. After 14 days of puromycin selection, infections were plated into separate dishes for Western blotting and the cell viability assay.

Western blotting: A375 cells were lysed in Cell Lysis Buffer (Cell Signaling 9803) with protease inhibitors (Sigma P8340). Lysates were homogenized using a Bioruptor sonicator (Diagenode) for 5 minutes (30s on-30s off cycle, high power) and then centrifuged at 15,000 rpm for 20 min at 4° C. Supernatants were quantified using the BCA assay (Thermo/Pierce). 20 ug of protein was denatured at 70C for 10 minutes before gel electrophoresis on a 4-12% Bis-Tris gel (Life Technologies). Proteins were transferred to nitrocellulose membranes at 60V overnight at 4° C. Antibodies used: Anti-NF2 (1:1000, Abcam ab109244), Anti-NF1 (1:1000, Abcam ab17963), Anti-MED12 (1:1000, Cell Signaling 4529S), Anti-CUL3 (1:1000, Cell Signaling 2759S), Anti-TADA2B (1:1000, Sigma HPA035770), Anti-GAPDH (1:5000, Cell Signaling 3683S). Membranes were developed by SuperSignal West Femto ECL (Thermo/Pierce) and imaged using BioRad ChemiDoc MP imaging system.

Cell viability assay: lentiCRISPR-infected A375 cells were plated in quadruplicate into 96-well plates at a density of 5×10³ cells per well. Either PLX or vehicle (DMSO) was added 1 day after plating. PLX was added at the following concentrations: 20 nM, 200 nM, 2 uM, 20 uM, and 200 uM. Drug/vehicle was renewed every 2-3 days using a Janus liquid handler (PerkinElmer).

After 5 days of drug/vehicle treatment, cell viability was measured using CellTiter Glo (Promega). After allowing cells to reach room temperature, media was aspirated from the cells and CellTiter Glo (diluted 1:4 in phosphate-buffered saline) was added. Plates were placed on an orbital shaker for 2 min followed by a 10 min room temperature incubation. Luminescence was read out on an EnVision plate imager (PerkinElmer).

Flow cytometry analysis of GFP knockout or knockdown: lentiCRISPR with sgRNAs targeting EGFP (SEQ ID NOs: 73-76 and 50-51, respectively, in order of appearance) were cloned using the following sequences (annotated in FIG. 28):

EGFP sgRNA 1 GGGCGAGGAGCTGTTCACCG EGFP sgRNA 2 GAGCTGGACGGCGACGTAAA EGFP sgRNA 3 GGCCACAAGTTCAGCGTGTC EGFP sgRNA 4 GGAGCGCACCATCTTCTTCA EGFP sgRNA 5 GAAGTTCGAGGGCGACACCC EGFP sgRNA 6 GGTGAACCGCATCGAGCTGA

Four shRNAs targeting EGFP in a pLKO (puromycin-selectable) vector were used (Broad RNAi Platform):

EGFP shRNA 1 TRCN0000072194 EGFP shRNA 2 TRCN0000072181 EGFP shRNA 3 TRCN0000072201 EGFP shRNA 4 TRCN0000072198

Control lentiCRISPR contained no spacer sequence and control shRNA was null hairpin TRCN0000208001.

For both lentiCRISPRs and shRNAs, virus was produced using a similar protocol as presented above but without ultracentrifuge purification. HEK293T cells with a single copy of EGFP (Broad RNAi Platform) were infected on Day 0 and then analyzed by flow cytometry on Day 5 and Day 11 post-infection. Flow cytometry was performed on a BD Accuri C6 cytometer in 96-well plates. Analysis was done in FlowJo (Treestar) by first gating for viable cells using forward and side scatter and then gating the fluorescence histogram.

Sequencing data analysis and indel detection: Off target loci in the human genome were identified for individual spacers using the CRISPR design tool (available at the website tools.genome-engineering.org). On-target and off-target loci were PCR amplified using Herculase II Fusion polymerase (Agilent), normalized, and pooled in equimolar proportions. Pooled libraries were denatured, diluted to a 14 pM concentration and sequenced using the MiSeq Personal Sequencer (Illumina). Sequencing data was demultiplexed using paired barcodes, aligned to reference amplicons, and analyzed for indels as described previously. Indel length analysis was performed by mapping the distance between multiple short reference sequences in individual reads.

Aspects of the invention also encompass a two vector, genome-wide KO system. Details are as follows:

1) Applicants utilize A375 (BRAF V600E mutation-containing) cells having Cas9 alone integrated into the genome. This may be done with lentivirus but may also be done with other methods of integration (integrase, recombinase, transposase, etc.) Typically the integration cassette will include Cas9 and a selectable marker to make sure that only cells with Cas9 active are kept. For e.g., the vector is EF1a-Cas9-2A-Blasticidin. 2) The A375 cells comprising Cas9 are exposed to a library of viruses. Each virus has U6 driving one sgRNA (“spacer” or “guide”). Thus in this case, the library delivers only the guide instead of Cas9 plus guide. The rationale for this approach is that it may be easier to produce a high titer virus with only having to deliver the guide. In aspects of the invention it may be practical for large scale screening and virus production to have only the variable part (the guide, which is one of 65,000 different guides) in the library virus and keep the constant part (Cas9) out of the library. 3) The rest of the screen proceeds from this point identically to the single vector system as described in this example which may include the following steps: Adding PLX (drug targeted to BRAF with V600E mutation); Killing most of the cells; Letting the cells that survive grow out; Extracting genomic DNA and Performing next generation (next gen) sequencing to find out which guides conferred the ability to survive PLX selection. Applicants have utilized the two vector system to knock out EGFP and hence this two vector system may be applied to a full-scale screen.

Example 10: Improved Lentiviral Vectors and Genome-Wide Libraries for CRISPR Screening in Human and Mouse Cells

Initial genome-wide, targeted loss-of-function screens using the CRISPR (clustered regularly interspaced short palindrome repeats)-associated nuclease Cas9 in human and mouse cells have revealed new mechanisms of resistance to cancer therapeutics (including vemurafenib, etoposide, and 6-TG) and identified genes essential for cell survival. When compared to screens using genome-wide libraries of RNAi reagents, screens with Genome-scale CRISPR Knock-Out (GeCKO) libraries demonstrate higher consistency amongst unique reagents targeting the same gene and have a higher target validation rate among top screen candidates'.

Applicants sought to improve both the lentiviral packaging and pooled library design of Applicant's original CRISPR screening system as described in Example 9. In the system described in Example 9, a pooled library of synthesized oligonucleotides was cloned into a lentiviral backbone containing both the Cas9 nuclease and the target-specific synthetic short guide RNA (sgRNA). This lentiviral vector (lentiCRISPR v1) had a low titer and required concentration of the virus using an ultracentrifuge or ultrafiltration membrane before performing a screen. To create a new vector capable of producing higher-titer virus, Applicants removed one of the nuclear localization signals (NLS), codon-optimized the remaining NLS and P2A bicistronic linker sequence, and changed the placement of the U6-driven sgRNA cassette (FIG. 47A). This optimized vector (lentiCRISPR v2) has a 7.1-fold increase in functional viral titer over lentiCRISPRv1 (FIG. 47B).

To further increase viral titer, Applicants also cloned a two vector system, in which the Cas9 nuclease and the sgRNA library are delivered in separate lentiviruses with separate antibiotic selection markers (FIG. 47A). The new lentiGuide-Puro virus has a 127-fold increase in functional viral titer over the original lentiCRISPR v1 (FIG. 47B). The increased viral titers of lentiCRISPR v2 and lentiGuide-Puro will greatly reduce reagent costs for GeCKO screens and enable infection without the need for concentration of viral supernatant. Cas9-mediated gene knock-out of a genomically-integrated copy of EGFP is efficient with both new lentiCRISPR systems (FIG. 48).

In addition to the vector improvements, Applicants designed and synthesized new human and mouse genome GeCKO libraries (See Tables 2A, 2B, 3, 4, 5, 6, 7, 8 and 9). These new libraries have a uniform coverage of 6 sgRNAs for each gene with higher gene and exon coverage (Table M).

TABLE M Comparison of new GeCKO v2 human and mouse sgRNA libraries with existing CRISPR libraries. Shalem et al. Wang et al. (2014) GeCKO Yusa et al. GeCKO v2 GeCKO v2 (2014) library v1 library (2014) library human library mouse library Species human human mouse human mouse Number of genes 7,114 18,080 19,150 19,052 20,661 targeted Targeting 10 per gene variable variable 6 per gene 6 per gene constructs per (typically 3 to 4 (typically 4 to (3 in Library (3 in Library A, gene per gene) 5 per gene) A, 3 in Library B) 3 in Library B) Number of none none none 1864 1175 miRNA targeted Targeting n/a n/a n/a 4 per miRNA 4 per miRNA constructs per miRNA Control (non- 100 none none 1000 1000 targeting) sgRNAs Total sgRNA 73,151 64,751 87,897 122,417 130,209 constructs (65,386 in (67,405 in Library Library A, A, 62,804 in 58,031 in Library B) Library B) Viral plasmid Dual vector: Single vector: Dual vector: Single and Single and dual vector sgRNA only Cas9 and sgRNA only dual vector: vector: sgRNA lentiCRISPR lentiCRISPR v2 (lentiCRISPR v2 and and lentiGuide- v1) lentiGuide- Puro Puro

New GeCKO libraries target an increased number of genes with uniform coverage (6 sgRNAs per gene divided into sub-libraries with 3 sgRNAs per gene—see Tables 3, 4, 7 and 8). The GeCKO v2 libraries also contain sgRNAs that target microRNAs (Tables 5 and 9) and control sgRNAs (Tables 2A, 2B and 6) that do not target in the genome. The libraries have been cloned into lentiCRISPR v2 (which includes Cas9 in the same vector) and lentiGuide-Puro (sgRNA-only vector) and are available in either format.

Applicants also improved the calculation of off-target scores based on recent empirical data and added sgRNAs to target micro RNAs (miRNAs) by directing mutations to the mature hairpin structure. The GeCKOv2 human library described in the Example now covers 19,052 genes, which is almost 1,000 genes more than the original GeCKO library described in Example 9. The library is divided into 2 sub-libraries (A and B). Each sub-library contains 3 sgRNAs for all genes and 1000 control sgRNAs that do not target any sequence in the genome. Library A also contains 7288 sgRNAs to target 1864 miRNAs. Screens can be performed with the combined library (122,417 sgRNAs) with 6 sgRNAs per gene or with either sub-library. This flexibility allows use of a smaller sub-library in situations where cell numbers are limiting (eg. primary cells, in vivo screens) or both sub-libraries together for better coverage. Similar to the human genome-wide library, Applicants also designed a GeCKOv2 mouse library with 2 sub-libraries containing 3 sgRNAs for each gene. The human and mouse libraries have been cloned into lentiCRISPR v2 and lentiGuide-Puro and deep sequenced.

Lentiviral cloning and production: For determination of lentiCRISPR v1, lentiCRISPR v2, and lentiGuide-Puro viral titers, the following sgRNA targeting EGFP (with no known targets in the human genome) was cloned into all 3 lentiviral transfer vectors:

EGFP sgRNA (SEQ ID NO: 73) GGGCGAGGAGCTGTTCACCG

To clone the sgRNA guide sequence, plasmids were cut and dephosporylated with FastDigest BsmBI and FastAP (Fermentas) at 37° C. for 2 hours. Oligonucleotides for the EGFP sgRNA guide sequence (Integrated DNA Technologies) were phosphorylated using polynucleotide kinase (Fermentas) at 37° C. for 30 minutes and then annealed by heating to 95° C. for 5 minutes and cooling to 25° C. at 1.5° C./minute. Using T7 ligase (Enzymatics), annealed oligos were ligated into gel purified vectors (Qiagen) at 25° C. for 5 minutes. Cloned transfer plasmids were amplified using a endotoxin-free midi-prep kit (Qiagen).

To make lentivirus, the transfer plasmids were co-transfected with packaging plasmids pMD2.G and psPAX2 (Addgene plasmids 12259 and 12260), as described previously in Shalem, O. et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343, 84-87 (2014). Briefly, for each virus, a T-75 flask of 80% confluent HEK293T cells was transfected in OptiMEM (Life Technologies) using 10 ug of the transfer plasmid, 5 ug pMD2.G, 7.5 ug psPAX2, 100 ul of Plus Reagent (Life Technologies), and 50 ul of Lipofectamine 2000 (Life Technologies). After 6 hours, media was changed to D10 media, DMEM (Life Technologies) with 10% fetal bovine serum (Hyclone), with 1% bovine serum albumin (Sigma) added to improve virus stability. After 60 hours, viral supernatants were harvested and centrifuged at 3,000 rpm at 4° C. for 10 min to pellet cell debris. The supernatant was filtered through a 0.45 um low protein binding membrane (Millipore) and used immediately.

Lentiviral functional titration: Lentiviruses were titered in a functional assay by measuring puromycin resistance after transduction. For each viral construct, 2.5×10⁴ HEK293T-EGFP cells were transduced in suspension (i.e. during plating) with 10, 100, or 1000 ul of viral supernatant in wells of a 24-well plate. For lentiGuide-Puro transduction the HEK293T-EGFP cells also had a genomically-integrated copy of Cas9 from previous transduction with lentiCas9-Blast. Each transduction condition (construct and virus volume) was performed in triplicate. In each well, D10 culture media was added to make the final volume 1.5 ml. Cell without any virus added were also plated in six wells (3 wells for puromycin treatment, 3 wells as control).

At 24 hours post-transduction, media was changed to D10 with 1 ug/ml puromycin (Sigma) for all wells except the uninfected controls without puromycin. At 3 days post-transduction, cells in all wells were split 1:5 to prevent any well from reaching confluence. Except for the uninfected controls without puromycin, new D10 media was supplemented with 1 ug/ul puromycin. At 5 days post-transduction, all cells in the uninfected control wells treated with puromycin were floating/dead, which was verified using Trypan Blue exclusion (Sigma).

For the remaining wells, adherent cells were present and cell viability was measured using CellTiter Glo (Promega) following the manufacturer's protocol. After allowing cells to reach room temperature, media was aspirated from the cells and CellTiter Glo (diluted 1:1 in phosphate-buffered saline) was added. Plates were covered with foil, placed on an orbital shaker for 2 min, and then incubated for 10 minutes at room temperature. Luminescence was read out on an Synergy H4 plate imager (Biotek) using a 1 second integration time and auto-gain to utilize the full dynamic range of the detector. Positive controls (untranduced cells without puromycin) and negative controls (empty wells) were included in the assay.

Fold differences in titer between viral constructs were calculated using luminescence values. Specifically, comparisons were made between pairs of viruses for the same volume of supernatant. Only viral volumes for which cell survival was greater than 1% and less than 20% of control (untransduced) cells were directly compared. Assuming Poisson statistics, 20% cell survival imples that approximately 90% of cells surviving puromycin selection were infected by only a single virus.

Flow cytometry data was collected from the same set of infections using a BD Accuri C6 flow cytometer. Using FlowJo (TreeStar), cells were distinguished from debris and doublets by gating in forward vs. side scatter area plots. EGFP fluorescence was measured in the gated population from transduced and uninfected HEK293T-EGFP cells.

Design of new GeCKO libraries: Genome wide sgRNA libraries for the human and mouse genomes were designed using the following steps:

-   -   (1) Identification of conserved exons: For the human library,         RNA sequencing data from the Illumina Human Body Map 2.0 (GEO         accession number: GSE30611) was mapped to the reference human         genome (hg19) using TopHat v1.0.14 and transcripts were         reconstructed with Cufflinks v1.0.2. Exons expressed across all         tissues in the Illumina dataset were chosen as constitutive         exons for sgRNA targeting. In addition, for each gene, the first         and last exons were excluded along with any exon that contained         an alternative splicing site. For the mouse library, Applicants         chose constitutive exons as exons that are shared by all RefGene         (available at the website refgene.com/) transcripts for the same         gene. Applicants then chose for each gene, 4 constitutive exons         for targeting, in cases where there are not enough constitutive         exons Applicants added exons starting from the second coding         constitutive exon towards the end of the gene. In both mouse and         human coding exons where identified using the CCDS database         (available at the website ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi).     -   (2) Choice of sgRNA sequences: For each candidate exon, all         possible S. pyogenes Cas9 sgRNA sequences of the form (N)₂₀NGG         were listed as candidate targets. Each 20mer candidate sgRNA was         mapped to a precompiled index containing all 20mer sequences in         the human genome followed by either NGG or NAG. This mapping was         done using Bowtie short read aligner, allowing up to 3 base         mismatches.         -   Off target score was calculated as follows, as described in             Hsu, P. D. et al. DNA targeting specificity of RNA-guided             Cas9 nucleases. Nat Biotechnol 31, 827-832 (2013):         -   For a single off-target position:

$\mspace{20mu} {\text{?}\left( {1 - {W\left\lbrack \text{?} \right\rbrack}} \right) \times \frac{1}{\left( {{\text{?} \times 4} + 1} \right)} \times \frac{1}{\text{?}}}$ ?indicates text missing or illegible when filed

-   -   -   Then these are aggregated as follows:

$\mspace{20mu} {S_{guide} = \frac{100}{100 + {\text{?}\text{?}\left( h_{i} \right)}}}$ ?indicates text missing or illegible when filed

-   -   -   W: weight of the location of base mismatch (from Hsu, P. D.             et al. DNA targeting specificity of RNA-guided Cas9             nucleases. Nat Biotechnol 31, 827-832 (2013)).         -   d: mean pairwise distance between mismatches.         -   n_(mm): number of mutations         -   S_(hit)(h_(i)): the score for a single off-target         -   Applicants then chose for each gene 6 sgRNAs such that there             were no more than 2 sgRNAs per exon.

    -   (3) Targeting of mature miRNAs: For the design of miRNA         targeting guides Applicants took the hairpin miRNA sequence         coordinates from the mirBASE database (available at the website         mirbase.org). Applicants then listed all the possible (N)₂₀NGG         sequences and chose 4 sgRNAs per miRNA preferentially choosing         sgRNAs that target the stem region in the stem loop.

GeCKO library pooled synthesis and cloning: DNA oligonucleotide library synthesis was completed on a programmable microarray using a B3 Synthesizer (CustomArray) and SAFC Proligo reagents (Sigma), as recommended by the manufacturer. The synthesis products were cleaved from the microarray and deprotected by overnight incubation in 28-30% ammonium hydroxide at 65° C., dried, resuspended in 30 ul TE buffer and then purified using a QIAquick spin column (Qiagen). Full-length oligonucleotides (74 nt) were amplified by PCR using Phusion HS Flex (NEB). For the PCR reaction, the manufacturer's protocol was followed using 0.1 ul of synthesized oligonucleotide template, primers Array F and ArrayR (see below), an annealing temperature of 63° C., an extension time of 15 s, and 20 cycles. After PCR, the 140 bp amplicon was size-selected using a 2% agarose E-Gel EX (Life Technologies, Qiagen).

ArrayF (SEQ ID NO: 77) TAACTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGAC GAAACACCG ArrayR (SEQ ID NO: 78) ACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCT AGCTCTAAAAC

The vector backbone (lentiCRISPR v2 or lentiGuide-Puro) was digested with BsmBI (Fermentas) and treated with FastAP (Fermentas) at 37° C. for 2 hours and gel-purified on a 1% E-Gel EX (Life Technologies, Qiagen). A 20 ul Gibson ligation reaction (NEB) was performed using 10 ng of the gel-purified inserts and 25 ng of the vector (for lentiCRISPR v2) and using 5 ng of the gel-purified inserts and 25 ng of the vector (for lentiGuide-Puro). From the ligation, 0.5 ul of the reaction was transformed into 25 ul of electrocompetent cells (Lucigen) according to the manufacturer's protocol using a GenePulser (BioRad). To ensure no loss of representation, sufficient parallel transformations were performed using the same ligation reaction and plated onto 245 mm×245 mm plates (Corning) with carbenicillin selection (50 ug/ml), which yielded 30-200× library coverage. Colonies were scraped off plates and combined before plasmid DNA extraction using Endotoxin-Free Plasmid Maxiprep (Qiagen).

Library sequencing and validation: To check library representation, synthesis fidelity, and bias, libraries were amplified and then deep sequenced. First, libraries were PCR amplified for 16 cycles using Phusion Flash High-Fidelity (Thermo) with primers to add adaptors for Illumina sequencing. For all libraries, PCR reactions were performed in duplicate and barcoded to allow quantification of bias introduced by PCR. Samples were sequenced on a MiSeq following the manufacturer's protocol using a v3 150 cycle kit with 10% PhiX (Illumina).

PCR replicates were demultiplexed using FASTX-Toolkit (Hannon Lab, CSHL) and adaptors were trimmed using cutadapt to leave only the sgRNA guide sequence. Alignment of the guide sequence to the appropriate GeCKO library index was done using Bowtie with parameters to tolerate up to a single nucleotide mismatch. The Bowtie alignment was then read into Matlab for further analysis (Mathworks). For all libraries, greater than 90% of sgRNAs were represented with at least one sequencing read and the difference in representation between the 90^(th) and 10^(th) percentile sgRNAs was always less than 10-fold.

Vector maps and reagent distribution: All lentiCRISPR plasmids (FIGS. 49, 50 and 51) and GeCKO libraries are available on Addgene and vector maps are available at the website genome-engineering.org/gecko/.

Design specification on changes between lentiCRISPRv1 and lentiCRISPRv2 are indicated below. The lentiCRISPRv2 encompasses the following aspects:

-   -   Novel hybrid LKO/FUGW design         -   5′ lenti elements and backbone are from FUGW,         -   3′ lenti elements are from LKO (Applicants took this             approach because the 3′ lenti elements in LKO have less             wasted space after WPRE)     -   Human codon-optimized FLAG tag was moved to C term of Cas9     -   Removed N-terminal NLS     -   Removed 2 residue linker between Cas9 and 2A         -   A convenient restriction site (BamHI) is now integrated at             beginning of 2A sequence     -   Unique human codon-optimized NLS     -   Unique human codon-optimized P2A     -   Moved U6 Pol3 cassette to after cPPT. Now directly upstream of         EFS Pol2 cassette.     -   Enzyme sites for easy modular removal of Pol3 cassette, Pol2         promoter, Cas9 CDS LTR-LTR distance is now 8.2 kb: This is >100         bp shorter than the lentiCRISPRv1 vector.

Applicants have shown that these improved lentiCRISPR vectors and human and mouse libraries will make it easier to perform GeCKO screens with enhanced lentiviral delivery options and greater choice over library size for different screening applications.

Example 11: Generation of Gene Knockout Cell Library

This example demonstrates how to generate a library of cells where each cell has a single gene knocked out:

Applicants make a library of ES cells where each cell has a single gene knocked out, and the entire library of ES cells will have every single gene knocked out. This library is useful for the screening of gene function in cellular processes as well as diseases.

To make this cell library, Applicants integrate Cas9 driven by an inducible promoter (e.g. doxycycline inducible promoter) into the ES cell. In addition, Applicants integrate a single guide RNA targeting a specific gene in the ES cell. To make the ES cell library, Applicants simply mix ES cells with a library of genes encoding guide RNAs targeting each gene in the human genome. Applicants first introduce a single BxB1 attB site into the AAVS1 locus of the human ES cell. Then Applicants use the BxB1 integrase to facilitate the integration of individual guide RNA genes into the BxB1 attB site in AAVS1 locus. To facilitate integration, each guide RNA gene is contained on a plasmid that carries of a single attP site. This way BxB1 will recombine the attB site in the genome with the attP site on the guide RNA containing plasmid.

To generate the cell library, Applicants take the library of cells that have single guide RNAs integrated and induce Cas9 expression. After induction, Cas9 mediates double strand break at sites specified by the guide RNA. To verify the diversity of this cell library, Applicants carry out whole exome sequencing to ensure that Applicants are able to observe mutations in every single targeted gene. This cell library can be used for a variety of applications, including who library-based screens, or can be sorted into individual cell clones to facilitate rapid generation of clonal cell lines with individual human genes knocked out.

Example 12: Plasmid Genome-Wide Libraries Comprising a Plurality of Unique Guide Sequences

The following plasmid libraries were deposited with ATCC on Jun. 10, 2014:

-   -   GeCK1—library of sgRNA plasmids each encoding selected guide         sequences and cloned into vector (lentiCRISPRv2)—ATCC Deposit         No. PTA121339;     -   GeCKO2—half library A (human) sgRNA plasmids each encoding         selected guide sequences and cloned into vector—ATCC Deposit No.         PTA121340;     -   GeCKO2—half library B (human) of sgRNA plasmids each encoding         selected guide sequences and cloned into vector—ATCC Deposit No.         PTA121341;     -   GeCKO2—half library A (mouse) sgRNA plasmids each encoding         selected guide sequences and cloned into vector—ATCC Deposit No.         PTA121342; and     -   GeCKO2—half library A (mouse) sgRNA plasmids each encoding         selected guide sequences and cloned into vector—ATCC Deposit No.         PTA121343.

The deposited libraries comprise pool of vectors each comprising sequence encoding a individual guide sequence of library useful according to the present invention, namely that may be used in the libraries, methods and/or kits of the present invention. The guide sequences are capable of targeting a plurality of target sequences in genomic loci, wherein the targeting results in a KO of gene function.

While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

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What is claimed is:
 1. A method for identifying one or more genomic loci associated with drug resistance, comprising: contacting a population of cells with a composition comprising one or more vectors that encode (a) a Cas9 protein and (b) a plurality of CRISPR-Cas system guide RNAs targeting a plurality of different genomic loci; selecting cells successfully transduced with the vectors, wherein the selected cells each comprises a CRISPR-Cas system comprising the Cas9 and the guide RNA; treating the selected cells with a drug to obtain cells having resistance to the drug; and profiling the depletion or enrichment of the guide RNAs in the cells having resistance to the drug by high-throughput sequencing to identify one or more genomic loci associated with the resistance to the drug.
 2. The method of claim 1, wherein the cells are eukaryotic cells.
 3. The method of claim 2, wherein the cells are mammalian cells or human cells.
 4. The method of claim 3, wherein the cells are cancer cells or stem cells.
 5. The method of claim 1, wherein the cells are transduced with a multiplicity of infection (MOI) of 0.3-0.75
 6. The method of claim 1, wherein the cells are transduced with a multiplicity of infection (MOI) of 0.3-0.4.
 7. The method of claim 1, wherein the Cas9 is Streptococcus pyogenes Cas9.
 8. The method of claim 1, wherein the Cas9 is Staphylococcus aureus Cas9.
 9. The method of claim 1, wherein the Cas9 and the guide RNA are encoded in the same vector.
 10. The method of claim 1, wherein the Cas9 and the guide RNA are encoded in different vectors.
 11. The method of claim 1, wherein the vectors are lentivirus, adenovirus, or adeno-associated virus vectors.
 12. The method of claim 1, wherein the composition comprises vectors encoding 100 or more different guide RNAs.
 13. The method of claim 1, wherein the composition comprises vectors encoding 1,000 or more different guide RNAs.
 14. The method of claim 1, wherein the composition comprises vectors encoding 20,000 or more different guide RNAs.
 15. The method of claim 1, wherein the drug is a cancer drug.
 16. A method for identifying one or more genomic loci associated with cell survival comprising: contacting a population of cells with a composition comprising one or more vectors that encode (a) a Cas9 protein and (b) a plurality of CRISPR-Cas system guide RNAs targeting a plurality of different genomic loci; selecting cells successfully transduced with the vectors, wherein the selected cells each comprises a CRISPR-Cas system comprising the Cas9 and the guide RNA; applying an selective pressure to the selected cells to obtain cells survived under the selective pressure; and profiling the depletion or enrichment of the guide RNAs in the cells survived under the selective pressure by high-throughput sequencing to identify one or more genomic loci associated with survival under the selective pressure.
 17. A method for identifying one or more genomic loci associated with a phenotype comprising: contacting a population of cells with a composition comprising one or more vectors that encode (a) a Cas9 protein and (b) a plurality of CRISPR-Cas system guide RNAs targeting a plurality of different genomic loci; selecting cells successfully transduced with the vectors, wherein the selected cells each comprises a CRISPR-Cas system comprising the Cas9 and the guide RNA; applying an selective pressure to the selected cells to obtain cells having a phenotype; and profiling the depletion or enrichment of the guide RNAs in the cells having the phenotype by high-throughput sequencing to identify one or more genomic loci associated with the phenotype. 